Friday, May 30, 2008

Greasy lazy pythons

How rich is it that when various woomongers try to fill their cracked pots with abiotic oil, one of their favorite processes is serpentinization?

Come on guys, how about some effort. If you’re gonna sell snake oil, fine. But isn’t it a bit obvious associating snake oil with serpentinites? At least pretend it comes from lizardite*. Or crocodilite. As it is, you're giving yourselves away.

*In a nomenclatural twist designed to foil zoologists, lizardite is a serpentine, while crocidolite is not.

Not a Koala

Just in case anyone out there mixes up large tree-dwelling animals.

Tuesday, May 27, 2008

Stuff left to do on this paper

make tables
format tables
decide which values to normalize to*
sort out references
streamline methods section
keep optional figures.
Wait for co-author to send me his paragraph.
Get feedback from boss.
Reformat references once target journal is confirmed.

*I've used the oldest, most widespread, most comprehensive, and least correct literature values for my reference materials. I'm hemming and hawing about whether or not it is worth changing, as the composition isn't that important to this particular paper- Homogeneity is vital, but the exact number doesn't really matter as long as it is constant.

and then I can get back to blogging, housework, and/or life.

Saturday, May 24, 2008

Your kids are poisoned. Deal with it.

The Australian newspaper reports that:

“Queensland health has refused to conduct extensive soil and water testing in Mount Isa despite its own study confirming 11 percent of children in the town have dangerously high levels of lead in their blood…
...Instead, the Queensland Health report recommended that a “living with lead” alliance – made up of government, council, and mine representatives – develop more “mitigation strategies”...

Lead poisoning causes brain damage in children, resulting in behavioral and learning problems. Traditionally, it is prevented by not poisoning the kids in the first place, but actually asking Xstrata to meet the same environmental standards as the rest of us must be economically disadvantageous, so they want to mitigate instead. I wonder, how do you mitigate against brain damage?

Some possibilities:
  • Remedial math lessons for kids (remedial ethics for mine execs is optional).
  • Heavy metal scavenger hunt (according to the report, they “could not find a source of the contamination”).
  • Brain damage? Well duh! They’re from Queensland!
  • Give the kids careers as labor ministers, or Queensland Health professionals.
On a more serious note, this sort of thing makes me wonder how much “economies of scale” are actually “economies of graft”. The theory says that bigger companies can be more profitable because they can use size to be more efficient. But in the case of Mt. Isa, the company simply uses its size to ignore environmental laws and poison any children that get in its way. If a company is the biggest dog in town, then it is not surprising that, as was the case here, Xstrata was able to vet the government press releases on this matter. As local labor MP Betty Kiernan said, “We wanted a partnership.”

Needless to say, if big companies can have “partnerships” instead of compliance, they have an advantage over those of us who actually have to obey laws. But the real pisser is when well meaning but ignorant activists assume that the answer is more regulation. Because then we end up with one more layer of rules that we have to follow while the bad guys can simply ignore, vet, or mitigate.

Wednesday, May 21, 2008

Reference management system open thread

When I was a student, I used endnote to organize and manage all of my references. In hindsight, this was probably one of the stupider decisions that I made. It meant that as soon as I finished and left university, the index that I spent 4 years building turned into an unreadable file, and I was left with the 14 pages in the back of my thesis as the only hint as to what my filing cabinet of papers contained.

While it would be melodramatic so say that this was a main contributor towards my poor record in publishing mostly finished work, it is one more annoyance that I don’t really need. And this year I am trying to make a renewed effort to get some manuscripts out the door- both old stuff that is still relevant, and recent stuff from my old university job.

I’ve heard all sorts of odd-sounding names when the subject of reference management comes up- words with non-transparent meanings, like Zotero, or JabRef (the indexer of choice for smugglers on Tatooine?). I have no idea what any of these things are. So I’m asking y’all to pitch in. Do you use a non-institutional program to manage your references? If so what is it? And most importantly, is it the sort of thing that is accessible to a computer semi-literate like me?

Tuesday, May 20, 2008

Help save the Australian solar industry

One of the less well-known features of the budget announced last week was the means testing of the solar energy rebate. Starting July 1, households with a combined income over $100,000 will no longer qualify for this rebate. Losing the rebate can increase the price of solar power by up to 200%. And with today’s interest rates (our mortgage repayments have doubled since we bought our house- how about yours?), most people on a combined income of less than $100,000 can’t afford solar even with the rebate. So this proposal will basically kill the domestic urban solar business in Australia.

The most straightforward approach to stop this from happening is to ask the Coalition to block the means testing in the senate. It is obvious to both the supporters and detractors of the Coalition that their response to the budget hasn’t been terribly effective so far; this will give them a badly needed win.

The Greens have already come out against this cut. If the Coalition joins them, then Labor will actually have to defend their decision to cut solar in favor of increased coal subsidies. If we’re lucky, that might mean that the Greenhouse and Environment Ministers will have to start answering questions on this issue, instead of ducking them.

How to do it:

  • Look up your senators (Wikipedia has a list).
  • Google the contact info for the listed Liberal and National senators from your home state.
  • Send them a short snail mail or email asking them to block the means testing of the solar rebate in the Senate.
  • Ask your friends to do the same- even if their politics differ from yours, this is an issue which should appeal to just about everyone who isn’t a coal-fired denialist Ruddbot.
  • Sending a thank you note to your Greens senators for opposing this measure wouldn’t hurt either.

Note: While I am a proponent of bringing nuclear power to Australia, I still think that energy diversity is important, and cutting renewables to fund clean coal corporate handouts is shortsighted.

Monday, May 19, 2008

RIP Tom Krogh

Professor Tom Krogh died late last month. He was the father of modern zircon U/Pb geochronology, and his contributions are easier to illustrate than to tell.

In 1970, when he started working on the U/Pb system in zircon, the smallest single zircon grain that could have its age determined was about this size:

As a result of professor Krogh’s achievements, grains considerably smaller than the ones below can now be analysed using solution chemistry.

But size isn’t everything. He also pioneered chemical and physical abrasion techniques for removing the metamict portions of zircons, allowing the resulting material to be dated more accurately due to the elimination of isotopically open material.

As one of my old bosses said, though, “He wasn’t just good. He was one of the good guys.” While the business of geochemistry can sometimes be secretive, possessive, and petty, Krogh acted in the interest of science. We are all better off as a result.

His son has set up a remembrance page here.

Saturday, May 17, 2008

Limerick Friday

It is Saturday evening here, but in the far western reaches of America it is still Friday, so here is a limerick for the founder of the day:

The science of mutating rhymes'
been unearthed by DC many times.
But without his oddity
He'd be a commodity
and sold off for nickels and dimes.

Click image to enlarge.

Thursday, May 15, 2008

Titanium as a cathodoluminescence activator in alkali feldspars

Ian Parsons, David A. Steele, Martin R. Lee, and Charles W. Magee 2008. Titanium as a cathodoluminescence activator in alkali feldspars American Mineralogist, Volume 93, pages 875–879

Albite patches in coarsely mesoperthitic alkali feldspars from the Klokken syenite have oscillatory zoning seen at blue wavelengths using cathodoluminescence. Using a five-spectrometer, high-resolution elemental mapping technique in an electron probe, we show a close correspondence between CL emission intensity and Ti, present at levels up to ~200 ppm. Albite patches were analyzed for major and 16 trace elements by laser-ablation inductively coupled-plasma mass spectrometry. SEM elemental maps acquired simultaneously with the CL showed that a similar zoning pattern is exhibited by Ca, but there is no correlation between CL intensity and Ca concentration. None of the trace elements analyzed correlate with Ti. We conclude that tetrahedral Ti4+ is the most likely activator of blue luminescence in these albitic alkali feldspars possibly because of a defect associated with Al-O-Ti bridges.

word cloud:

created at

This is an example of a low marginal cost paper. The main purpose of bringing the samples to the ICP lab was a different study, but Ian figured he might as well check this out while everything was in place. The main study was big, complicated, and only just recently went off to reviewers. But this was simpler and more straightforward, so got written up and published first. So it is a great example of why research needs to be structured in a way such that investigators can veer off of their predetermined path if they see the opportunity to potentially figure something out for relatively little time, effort, and cost.

Saturday, May 10, 2008

Trace elemental analysis of a big night out

brown beer bottle <LOD621242428 <LOD <LOD1534 <LOD563251
green beer bottle <LOD575730 <LOD <LOD <LOD2483126129899
brown beer bottle <LOD701212319 <LOD <LOD1834 <LOD455145
fancy wine glass <LOD9428136526037262 <LOD <LOD <LOD10179
green wine bottle <LOD70892416 <LOD <LOD1329 <LOD911156
clear Southern Comfort bottle
<LOD444107 <LOD <LOD <LOD <LOD303 <LOD <LOD 244
white porcelain (Ooops!)527.832512851547852110480878 <LOD150545
all units ppm (mg/kg).

When drinking from fancy wine glasses, it is imperative to chug your wine before it can leach anything out of the glass.

On a related note, if you break such a glass, DON'T RECYCLE IT! High lead glasses are fairly harmless if they sit empty most of the time, but if they come back as vinegar or baby food bottles?

U/Pb geochronologists of a certain flavour like to laud zircon as the king of minerals, with unmatched longevity, retention, and complexity. The last analysis adequately describes how society in general feels about this mineral, which is the source for all industrial zirconia.

Disclaimer! This is a synthetic data set, meaning that either the numbers, and/or the implied conditions of analysis are made up. The data is real, but you'll have to get me drunk before I spill the methodological beans. DO NOT operate analytical equipment that uses high voltage or ionizing radiation while smashed. It creates too much unnecessary work for the poor technician who has to come in and fix everything the next morning.

Thursday, May 08, 2008

Another reason I’m glad I left Sydney

According to the news, a motorist jumped on the brakes after pulling in front of a 50 bike peleton in Sydney this working. The resulting pile-up included half a dozen former and current Olympic riders, a jack-knifed semi-trailer, and Kate Nichols, who had only just returned to riding after being injured in the German 2005 crash that killed Amy Gillett. Thankfully nobody was killed this time. It ain’t just motorists who have such a callous disregard for human life, either. Yesterday, also in Sydney, two teenage pedestrians were arrested from throwing a boulder off of an overpass at a car below. The arresting officer was patrolling on a bicycle.

Monday, May 05, 2008

Research paper word clouds

Brian at Clastic Detritus has word clouded two of his papers, creating what has to be the coolest word cloud use ever. Having no shame, I am going to copy him.

Here is Birch et al. 1997:

created at

Here is Klemme et al. 1998:
created at

Note that both papers pass the suck-up test- the PhD advisor's name (from references) is not a prominent word. This is unsurprising, given that the people who actually wrote these papers haven't been students for some time.

The appearance of Sutherland raises a self-referential alert in Birch et al., but other than that the lists seem pretty topical.

Now I need to get some of my own manuscripts submitted so that I can do this on them!

Saturday, May 03, 2008

Musical interlude

I really need to get some work done on a paper, do real work, get family time, etc., so I'll leave you with this musical quiz meme courtesy of sciencewoman:

The rules:
Step 1: Put your MP3 player or whatever on random.
Step 2: Post the first line from the first 25 songs that play, no matter how embarrassing the song.*
Step 3: Post and let your magnificent readers guess what song and artist the lines come from.
Step 4: Strike through when someone gets them right
Step 5: Looking them up on Google or any other search engine is now considered fair game, as the post is very stale.

*I have altered the methodology by excluding songs where the first line is the name of the song.
(drum roll)

12.Cue the music, curtain falls
15.How long how long how long/ will we take to come undone
10.This wide brown land’s a crock of shit
11.Humpty Dumpty sat on a wall
13.Made a promise to myself
14.Quando você passa eu sinto seu cheiro
24.Ain’t no talkin’ to this man (Let him fly; Dixie chicks) - rebecca
9.Ninguém passa aqui sem cantar samba-reggae
5.Somewhere a strut
3.I’m ready / I'm ready for the laughing gas (Zoo station -U2) - jrepka
23.You’re dangerous ‘cause you’re honest (Who’s gonna ride your wild horses; U2) -sciencewoman
---Voyager 2 at Neptune---
25.I know/ that the sunset empire shutters and shakes
16.You never called
22.Many is the time I’ve been mistaken (American Tune - Simon & Garfunkel) -Sachqua
E.C. You're a real tuff cookie with a long history (Hit me with your best shot- Pat Benatar) - Tuff Cookie
20.Good morning the worm, your honor (The Trial Pink Floyd) - Steve Bloom
19.You know that I care
18.I’m sailing away (Come Sail Away; Styx)-jrepka
7.Billy Rose was a low rider (Prison Trilogy- Joan Baez)- silver fox
--Apollo 11---
17.Here you’re comin’ on so nice to me
21.Let’s all get up and dance to a song (Your mother should know; beatles) - jrepka
6.The day breaks
1.Well East coast girls are hip (California Girls- beach boys)-Ecogeofemme
4.We-e-e-e-e-ellllllll / You know you make me wanna (Shout Isley brothers) - Tuff Cookie
2.She comes on like a rose

And, for extra credit, a line for everybody's favorite igneous blogger: (see 1980)

In an effort to assist the local sedimentologists, I've put the songs in stratigraphic order, with a few space age marker beds. Still left:
1 Beatles song, 1 Pink Floyd song, all 3 Australian and both Brazilian artists.

Friday, May 02, 2008

Carnival of space

The first anniversary issue of the carnival of space is up at Why Homeschool.

Thursday, May 01, 2008

Thorium / uranium ratios and atomic power

Thorium and uranium are the only two actinide elements that are stable enough to have survived since the formation of the solar system without being destroyed by radioactive decay. They are geochemically similar. Both are strongly lithophilic, meaning that they form oxides and dissolve into silicate melts, without entering into metallic or sulfide phases. Both elements are fairly refactory, meaning that they condense earlyish in the solar nebula. And they are both incompatible during mantle melting. This means that they do not fit into the crystal structure of mantle minerals, so when a planetary mantle undergoes partial melting, the vast majority of the U and Th dissolves into the melt, and relatively little remains in the mantle mineral residue. This is because Th and U are both large +4 cations under most conditions, and mantle minerals (made mostly of Mg, Si, Fe, Al, and Ca oxides) don’t have any crystallographic sites into which such ions can fit.

Of the two, Th is slightly more refactory and incompatible, but not much, so their ratio doesn’t change a whole lot. As a result, the solar ratio (about 4) is not that different to the ratio of the lunar crust, the Martian crust, the Earth’s crust, and the Earth’s mantle. For most meteoritic, igneous, and mantle rocks, Th/U is about 4.

This number seems to have been picked up on by the more extreme proponents of nuclear fission- generated electricity, as evidence that even if we run out of uranium, there is still lots more thorium. Technically, this is true. If we were to run the entire solar system through a refining mill with a 100% recovery percentage, then at the end of the project, we would have 4 times more thorium than uranium. But the real world doesn’t work like that.

Even though the crustal Th/U ratio is also about 4, we aren’t conceivably going to dig up the entire Earth’s crust either. So the bulk crustal (or planetary) Th/U ratio is not really relevant to anything other than science fiction. What is important is the ability of geological processes to concentrate these elements into a highly enriched deposit, which we can then mine for a reasonable cost and effort. And this is where U and Th start to differ.

Although these two actinides are geochemically similar under most conditions in the solar system, there is one key difference in their chemistry. In the presence of abundant oxygen, U can oxidize from +4 to +6. For the first two billion years of Earth’s history, this was irrelevant. But about 2.4 billion years ago, free molecular oxygen first started appearing in Earth’s atmosphere and surface waters. And this changed everything.

Thorium can’t form a +6 ion, because Th +4 has the same electron configuration as the noble gas radon- all the electron shells are closed. But uranium has 2 extra electrons to lose, given enough oxygen around to take them. And the hexavalent chemistry is quite different to the tetravalent. In the +4 valence, both U and Th are generally insoluble under most hydrologic conditions. But U +6 forms a uranyl ion (UO2++), which is highly soluble in most geologically reasonable waters.

As a result, for the last 2.4 billion years, uranium has been dissolving from oxidized rocks, flowing through aquifers with the groundwater, and then reprecipitating wherever a later chemical reaction consumes the oxygen in the water. What this means is that uranium can be- and is- concentrated by a geologic process which has no effect on thorium.

The result is that uranium forms deposits more frequently, and of higher grade, than does thorium, which is distributed much more evenly across a wide variety of rock types. Today the world has a uranium reserve of 4 million tonnes, with a resource maybe ten times larger. This is despite not actively exploring for the substance since the cold war ended. Thorium, strictly speaking, doesn’t have reserves at all; it is currently only recovered as a byproduct of rare earth element mining. But based on known occurrences of monazite (LREE)PO4, which can contain a few percent of Th), the estimated resource is about 1.5 million tons.

So although the bulk crustal concentration of thorium is higher than that of uranium, its simpler chemistry means that it does not get concentrated into mineral deposits as easily. So while claiming that Th is more abundant is technically correct, it isn’t the sort of technicality that one should base energy policy on.
[edit: typos]