Sunday, March 29, 2015

Geosonnet 27

Selenium is sulfur’s sober mate,
Not lost to vapor bubbles of the mind
In rock or water, should one saturate
They stay together, besties of a kind.
Se cannot be photosynthesized
To form selenate in anoxic seas
From fractionation, we hypothesize
an oxic whiff in late Archean breeze.
The isotopic signal is preserved
when anions are partially reduced.
Complete reduction, ratios are conserved
No atmospheric signal’d be produced.
   But choose your sample wisely, and you’ll see
   The right technique reveals its history


Geology 43 259

Other geosonnets: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64  65 66

Tuesday, March 24, 2015

Taking a PhD into the real world

Here in Canberra, the “Science meets Parliament” event is running.  I am not attending- the luminaries and power players can do their thing, but out on the wrong side of the tracks, our factory needs to keep putting lasers on sharks for the good of the economy.  Luckily, some of the scientists there have taken to twitter, so snippets and thoughts are able to escape.  Given that engagement is one of the things on their agenda, I thought I would chime in.

One of the topics mentioned was non-academic careers for recently graduated science PhD holders.  As someone who has worked in academia, industry, and government since graduating a long long time ago, I figured I’d take the opportunity to chime in with my two cents.  Note, however, that this is only 0.000022% of the attendance fee for the event, so discount this advice accordingly.

As a result of the deprofessionalization of science, there are no longer copious private sector basic research jobs for scientists to graduate into.  They do still exist, but not nearly in the numbers required to take all the PhD students who are excess to the requirements of the academic machine. 

The other problem with this retreat by science into the ivory towers of academia is that people in the real world- including employers- are less likely to really understand what scientists do, and what specifically a PhD graduate has to offer.

When a person leaves university with their PhD in hand, they generally have three things:  A tacky outfit (gown, hat, etc), a body of in-depth knowledge that makes them the world expert in a very small field of study, and the ability to do research.  Only the third of these is a salable skill, except in extraordinary conditions. This puts students leaving academia in a very different boat than those continuing on to a post-doc, where expanding or leveraging your field of PhD study (the second thing) is standard practice.

As a result, PhD-holding job seekers can be a bit disoriented.  This leads to all sorts of sad situations, including those where graduates leave their degrees off of their CV’s in hopes that this makes them more employable.  However, this is a suboptimal solution.

Furthermore, being able to figure things out which aren’t known is a really useful skill in a variety of situations.  Even with Wikipedia in our phones, understanding basic derivations lets us estimate things faster than fingers can tap screens. It lets us solve problems that may not have ready solutions published in a publically available place; it lets us adapt to changing circumstances where the underlying issues are constant, but the specific combinations of problems is changing in a way that makes simply looking up a solution impossible.  Being able to figure out how the world works is a useful, marketable skill, but to be valuable to us we need to make sure that we don’t devalue it.

There are a few things that scientists entering the normal workforce need to remember.  Firstly, in private enterprise, time is money.  There is a bad habit in poorly supervised PhD programs to devalue a student’s time- basically tell them to take however long it takes them to do some particular task.  In private enterprise, where the accountants will be tracking your billable hours and balancing project budgets, it is very important to use time effectively.  Ask for help, communicate with your colleagues, copy what your predecessor did; all of these things are preferable to spending a week proving that you can independently derive shit. 

The corollary to this point is that you need to value your time, and make your employer and clients value it as well.  Earning a PhD takes years of study and effort- an outlay similar to becoming a doctor or a lawyer as a postgraduate course of study. Business people generally assume that things are- to some extent- worth what they cost; a person who charges himself out at marginally more than grad school rates will give the impression that he has little to offer.

Of course, the academic meatgrinder doesn’t want any of this to happen.  As long as academia thinks of PhD programs as molds for the next generation of instructors to be injected into, it will try to make them as cheap as possible.  This is why PhD graduate supply is high, demand is low, and employment tactics like adjuncting place downward pressure on wages and conditions.  Universities don’t want PhD’s to succeed; that will cost them money down the road.


Luckily, those of us in the Earth Sciences are in a position where, at least in Australia, there are plenty of other opportunities around.  Impoverishing your students only makes sense if you plan on eventually hiring them; if most of them are destined for careers outside of academia, then an academic institution gets the most benefit by having graduates get rich enough that they want to give money back to their schools. If enough scientists become professionals of some description or another, then the schools will eventually think of use as being more like lawyers than English majors, catch on, and put some effort into professional development of research students.  Until then, though, it is up to us to help each other.

Tuesday, March 17, 2015

Adventures in Open Access publishing

 There is not a lot of diversity in the journals geochemists, geochronologists and hard-rock petrologists traditionally publish in.  Precambrian Research, Geochimica, Chemical Geology, Gondwana Research, and EPSL are all run by Elsevier, while the Journal of Petrology and Contributions to Mineralogy and Petrology are also published by large, for-profit corporations.  American Mineralogist is one of the few society journals still published and operated independently. And although member subscriptions and not too dear, the journal is by no means open access.

Other fields of geoscience have been making more progress in the open access revolution.  Planetary and astronomy related geophysics often finds its way into arXiv, biogeosciences can sometimes access PLOS or PeerJ, and the EGU have a variety of open access society journals which span a range of geophysical topics.

One of these journals is Geoscientific Instrumentation,Methods, and Data Systems (GI). While most of their published work appeares to relate to home-made data acquisition systems for geophysical experiments, a colleague and I decided to approach them and see if they were interested in a manuscript relating to ICP-MS, one of the mainstay bread-and-butter methods of geochemical analyses these days. So we sent in the manuscript, and, to make a long story short, it is published online here.  

Anyone reading this who is interested in new, community-based alternatives to the big scientific publishing houses should check it out- the process and handling was similar to any other journal, the timescale was similar to traditional publishing in our field (about 5 months submit to published, including Christmas, and at least 1 month of delay which was entirely my fault), and I have to say that I found the editors to be as professional and helpful as anywhere else I have submitted.


 And the work I originally blogged about here a long, long time ago is finally in print.

C. W. Magee Jr. and C. A. Norris (2015) Alkali element background reduction in laser ICP-MS Geosci. Instrum. Method. Data Syst., 4, 75-80.
www.geosci-instrum-method-data-syst.net/4/75/2015/
doi:10.5194/gi-4-75-2015

Monday, February 23, 2015

Geosonnet 26

A fibrous rock which lodges in the lung,
Inhaling wisps of amphibole can kill.
While chrysotile's damp mantle story's sung
Asbestos brown and blue confuse us still.
Sheared plutons from the Miocene contain
Some common hornblende altered to cause death,
What process can infect a rock so plain
To make it threaten those who draw a breath?
The saline alteration of the rock
Iron oxidation turns to ferric
Plutonic amphiboles- corrupted stock
Fibrous blue and lethal by the skerrick.
   Las Vegas gambles every breath they hold
   Lest cancer deal, it's time that they were told.

Geology 43 63

Other geosonnets: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47

Saturday, January 31, 2015

Twenty-five sonnets over 4 billion years

For the last 6 months, I’ve been summarizing research articles from the high profile academic journal Geology in sonnet form; trying to distill the artistic meaning of the research, be it the methodology or the interpretations.  The first 25 of these sonnets are compiled below.


They are listed in stratigraphic order of the time period studied; that is, the sonnet about the study of the most recent rocks on top, with research on older rocks below.  The one sonnet describing a study of Martian rocks is listed last, as those rocks are probably older than any of the terrestrial studies described here.

These fall into five broad categories: The Way of the World (Lab studies, simulations, and Quaternary rocks), Climate and Carbon (Tertiary); Death on a Blue Dot (Cretaceous through Cambrian extinctions) Ice ( Ediacaran and Cryogenean), and The World Forms (the first 3.8 billion years).
  Numbers refer to the described paper, in terms of volume-page in the journal Geology. They are also linked, as are some technical terms.

The way of the world

The linear progressions we assume
sphericalize our precious holy cows
the certainty simplicities presume
breed dreamt-up facts we dutifully espouse.
Repeated careful data overthrow
and phosphorus impurities reveal
Olivine is white-hot Devil's snow
A closet skeleton time can't anneal.
This phoenix from volcano is reborn
Forgotten stories texture can unearth
abandon simple models, do not mourn
Complexity's explanatory worth.
   The simple models woo, but cannot stay.
   Eventually the facts get in the way.

40-447
The vast caldera of the Yellowstone
Erupts siliceous ash from time to time.
It’s far from the Cascade subduction zone
Therefore, a mantle plume’s the suspect prime.
But magma conducts electricity
Conductors in the mantle lie out west
The tomographic maps are quite pretty
But show no melt where theory would suggest
A plume, with mantle source below the crust
Should yield a seismic and conductive trace.
Because we can’t detect deep melt we must
Explain resistance far below this place.
   A pulsed hotspot, or plate-related stall?
   Or maybe plumes do not exist at all.

 42-771
The ants which scuttle by between our toes
Dissolve the min’rals of the Earth we tread
The calcic feldspar, slipped under their nose
Ten trillion insects weather, pit, and shred.
The Himalayan mountains cool the Earth
Though mangroves and the grasses do their part,
But ants may do what was the work of turf
By min’ralizing CO2, they start
Evaporating seas in Neogene
Drying the Earth to suit their sandy hives
Anthropocene becomes the Formicene
The terraformic swarm constructs, connives.
  No human teamwork makes emissions slow
  Yet toiling ants sequester far below.

42-759
The Vikings lived in Greenland 'till in cooled.
Ten thousand years before, as glac'ers thawed,
Melt water in the North Atlantic pooled,
The Younger Dryas cold snap shocked and awed.
In Norway, glaciers reappeared on high,
Above the fjords where stoic Norse rule lapsed.
Then Carolina icebergs floated by,
As Greenland outlet glaciers collapsed.
Why would cold make this icecap melt, not grow?
Emotionless wind froze the Baffin Bay.
Warm currents thawed the ice tongues from below;
Without a shelf, the glac'er sped away.
  Today such currents threaten the Antarctic
  An outburst would be deluge, not cathartic.

Discharged a hundred cubic miles yield
The timing of this eruption did bridge
Reversal of the Earth’s magnetic field.
We measure timing of this ancient blast
With argon from potassium decay
This cataclysm from the recent past
might warn us should another come today.
The crystals froze, then thawed, then froze again.
The magma chamber did not slowly stew
chronology of xenocrysts explain
What to expect, should this begin anew.
  The warning won’t be twenty thousand years
  to outburst, from when magma first appears.

Climate and Carbon

The sunset lion, as Britannia aged
Survived, with every man, the frigid waste.
Industrial hostility upstaged
The sanctity of souls, their wreck encased
In icy seas and grinding floes made cold
By deep Antarctic circumpolar flow.
Dark isolation froze this land, how old
Are continental glaciers, ceaseless snow?
Six desp'rate heroes sailed the Scotia Sea
Dead arc, live backarc ridge beneath their keel
Tectonic forces pulled their goal to lea,
Deflected currents, begat their ordeal.
  Endurance sank, endurance overcame
  Asylum, dawn, and cause were all the same.

41-963
A pox on all those proxies non-unique
Which make interpretation hard to do.
Magnesium to calcium we seek
Sea temp'rature, and not pCO2.
So lithium, uranium are used
to disambiguate the Mg curve
O. umbonatus data's not recused.
Antarctic ice growth isotopes observe,
But whence the melting in the Miocene?
Here isotopes of carbon join our tale,
And sedimentary burndown in marine
Organic carbon makes the icecap fail.
  Antarctic ice was thawed by CO2
  Let's try repeating this effect anew.

40-523
For fifty million years, ‘tis understood
A vanished forest froze in permafrost.
The isotopes of carbon in the wood
Tell secrets of the climate we have lost.
Then brackish duckpond, now a frozen sea,
Ex-crocodiles where Franklin did maroon.
Those Rains of Castamere, we can’t agree:
Cold drizzle or a tropical monsoon?
Extinct sequoia yearns for rain no more
Yet in its fossil rings it has preserved
A dryad’s weather journal, yielding lore
of summer rain and winter drought observed
  The Arctic Ocean’s lost half of its ice
  What happens when it’s gone? We need advice.

Death on a blue dot

Just Sixty-six million short years ago
(Though Deccan volcanism coincides)
The Yucatan was smote a cosmic blow
And the Gulf shelf collapsed in those fell tides
Late Cretaceous sediments were scoured,
Deposited as “boundary cocktail.”
Unsorted forams, lime mudstone, powered
By Chicxulub-induced collapse of shale
The wildcatters call the seismic line
“Middle Cretaceous Unconformity”
Not middle, end; deluvian, malign,
Complete destructive uniformity
  The Mesozoic ended with this splat
  So Gerta Keller, please hang up your hat

42-895
From flood basalt hot sulfur will exhale,
Across the dying planet, smog bank draped
The genie left the bottle, empty grail,
No evidence what long ago escaped.
The lava flows forget what they degassed
A fleeting daydream, lost with time’s progress
But though a hundred million years have passed
The clinopyroxene preserves the S.
Partitioning experiments defined!
A synchrotron or ion probe can see
The sulfur clouds to which we once were blind
Are quantified now, analytically.
   Sulfurous magma wrecked the biosphere
   While clean eruptions let life persevere.

41-955
The Central Atlantic Magmatic Province
Erupted tholiitic and potassic.
C O two upset atmospheric balance.
Eco-collapse ended the Triassic.
Green sulfur bacteria’s isotopes
Show photic zone euxinia prevailed.
Stomatal size decreased (show microscopes)
And carbon biomass was soon curtailed.
Compound-specific isotopes will tell
Which phytoplankton thrived in these tough times,
While wax from leaves and calcite from a shell
Record recovery in clastic slimes.
  The Triassic ended as it began
  Can those extinctions be surpassed by man?

42-779
The strontium which weathers from the land
Is held by teeth and shells beneath the waves
Their creatures live, then die, interred in sand
with isotopes in stratigraphic graves.
The greatest dying Earth has ever seen
Initiated the Triassic time
Before the ants evolved, rock weathering
Was temperature dependent, leaching lime.
Warm mud in post-apocalyptic waste
Bereft of vegetation, washed away.
And Gaia, both hungover and disgraced,
Left complex biomes for another day.
  She sobered up in five or six epochs
  But those hard times forever changed the rocks.
The Permian extinction was severe,
though only callous geos call it "great."
Sulfur and carbon choked the atmosphere
Siberian eruption exhalate.
A lava-coal explosion, it’s surmised
Spread fly ash all around the sickly Earth,
But if this ash is made by wildfire,
The evidence for coal fly ash is dearth.
A sulfate drought could set the world aflame,
The brimstone vapors choking off the rain.
The lava’s murder weapon’s not the same,
But "Lip" can improvise to kill again.
   If carbon, sulfur cycles stop their flow
   The ecosystem has nowhere to go.
On Mars and Venus air is CO two,
While on the Earth it is but a trace gas.
Our rocks and water scrub the gas into
The stable carbonates, which won’t degas.
In torrid climates, weathering is fast.
Cold rivers transport unreacted grains
Fluvial temperature in eons past
Can be deduced with XRF and brains.
The elements in sediments explain
An early Permian heats up and thaws.
Jokulhlaups warm up more than the jungle rain
Digesting rocks chewed up by glacial jaws.
   This weathering drew down the CO two
   But not enough for ice to grow anew.

42-711
The oxidation of the atmosphere,
And buffered ocean water do record
Life’s radiation into a frontier.
When proxies tell this tale, they are adored.
While sulfur oxidation can detect
Stagnation deep in Neptune’s dusky realm,
A noisy delta S makes us suspect
Metabolism signals overwhelm.
Portentous albatross foresaw the brine,
Which makes the sea the beverage of the dead,
Has sulfate contents greybeards can divine
With isotopes of calcium instead.
  The ocean’s respiration, waves to slab,
  Can be deciphered in a far off lab.

Australia is a dry and stable land.
No mountain range, no active slipping fault,
And yet this plain had lava seas erupt.
We call them Kalkarindji flood basalt.
It’s hard to know just when these rocks were formed.
The weathering and rock type complicates
Radiometric dates of dykes that swarmed
When seas contained the first protochordates.
For ten long years they searched the outback rocks
For grains unhurt since fossils first were formed.
In hopes the nucleii-related clocks
Survived half billion years, still undeformed.
  510 MA, a date of some distinction.
  Flood basalts can lead to mass extinction.

Ice

The Ediacaran saw creatures grow
Diversify as animals evolved.
But Cambrian descendants do not show
A lineage, preserved or else dissolved.
A missing fossil yearns to be dug up.
The Flinders Ranges burn to tell their tale
Trace fossils, both a spicule and a cup
Mean evolutionary theories can prevail.
Coronacollina was once a sponge
With opaline supports to hold it flat
Choia’s ancestor, before the plunge
Into the Cambrian destroyed the mat
  On which it lived, before it then evolved.
  Another fossil puzzle has been solved

42-815
The ozone and peroxide in the air,
enriched in isotope O seventeen,
Pass on the spike reaction products bear;
This stratospheric label’s not marine.
If limestone sulphate bears this airy mark
deceitful proxy! geosaboteur!
Thus reconstructed oceans fade to dark,
Eliminating tales that never were.
A lithologic memory withdrawn,
Built on assumptions hereby disallowed
The dreams of times hypothesized are gone
Mere fanciful illusions, disavowed.
  A lab revealed the havoc smog did wreak
  Perhaps they need a microbeam technique.

42-1103
The Earth once had a frozen shell of ice
encasing oceans, land, from pole to pole.
The mystery: what process could suffice
To kiss Snow White, rouse cryogenic soul.
One theory says volcanic CO2
Would slowly warm the Earth until the thaw
As ice breaks up, the air and water brew:
Carbonic acid forms: paleo-spa.
The isotopes of boron measure bases.
Post-glacial carbonates record the change
As acid forms, the calcium replaces
Hydronium, a weathering exchange.
   Across the world, the acid came and went;
   A single ocean-atmosphere event.

New biostratigraphic data may
Help Cryogenian stratigraphy
The timing’s known from rhenium decay
The vase shaped fossils match from every sea.
Were they amoebas wearing armor plate?
Or protist tanks, cilia on the brink?
Eukaryotic arms race tempted fate
Destabilizing carbon source and sink.
Darwinian selection did not give
Thoughtful reflection, cool restraint, or mirth.
Organics buried, still they strove to live,
Turned pale blue dot into a snowball Earth.
  Three quarters of a billion years ago
  The first nuclear winter: “Let it go…”

The world forms

Enough with carbon, climate variation
Let’s look at rocks from a far older time,
Which lacked much copper mineralization,
And when anorthosites were at their prime.
Earth’s middle age- boring for a reason?
Tectonics were remarkably unchanged.
Ice and iron were both out of season.
A billion years of uniform exchange
Of isotopes, strontium, and S
The active margins ringed the continent.
Slow, steady mantle cooling caused the process
Strong lithosphere held melts incipient
  It ended with Rodinia dispersion
  Which led to Earth’s exciting, current version.

42-619
Nobody studies fucking iodine.
The halogen too rare for us to care,
But iodate to carbonate’s inclined
So we might have a useful proxy there.
This IO3 requires oxygen,
And thus does not exist in reduced seas.
Its presence in old carbonates means then
Ozone and oxygen were in the breeze.
Archean carbonates do not have I,
But it appears when O first graced the air.
And thus another tool is forged, whereby
Our planet’s past can be unearthed to share.
  This gas we breathe controls the biosphere.
  We’d like to know what made it first appear.

42-923
Our early atmosphere was quite anoxic
‘till early algae terraformed the Earth.
One grand event, replacing gasses toxic?
Or did O oscillate since life’s first birth?
Did evolution make fate manifest?
Inexorable progress of the gene?
Or was the early oxygen repressed?
Methanogenic dominance was seen.
These visions of our past yearn to be fact.
Hypotheses distinct yet plausible.
The dawn of life’s mysterious, abstract,
Lest ancient rocks reveal what’s causable.
   Archean soil lets us know the way.
   Oxygen came, but then it went away.

42-747
The cratered lunar face preserves the song
Of bolide roller derbies eons past
But while the cold dead moon remembers long
The rains of Earth reshape the surface fast.
Did impacts peak four billion years ago?
Or taper off through geologic time?
Archean rocks are analysed to know
micaceous balls were hot glass in their prime.
This impact melt was blasted into space
By comets larger than the dino's doom.
Thus diminution models must replace
The cut-off LHB has us presume.
   Can cratering effect how cratons grow?
   Tectonic orogens changed status quo.

42-359
The Schrödinger bacteria’s Barsoom,
Where robots scan the wadi of the Styx.
There died, or never lived a microbe bloom
When déjà vu and Dejah Thoris mix,
Her hungry eyes fixed on Hadean seas,
Lowell’s canal dream just an aquifer.
The playa droid with X-ray vision sees;
Areocalcrete Earthings soon infer.
With carbonate and opal intergrown,
Australia’s prayer of cheap uranium,
As vengeful Ares, orbited by drone
Blends nukes and life within his cranium
  Thus Opportunity grinds sands of time
  Which mortals fancy Ceres made of lime.

Thursday, January 22, 2015

Geosonnet 25

The Earth once had a frozen shell of ice
encasing oceans, land, from pole to pole.
The mystery: what process could suffice
To kiss Snow White, rouse cryogenic soul.
One theory says volcanic CO2
Would slowly warm the Earth until the thaw
As ice breaks up, the air and water brew:
Carbonic acid forms: paleo-spa.
The isotopes of boron measure bases.
Post-glacial carbonates record the change
As acid forms, the calcium replaces
Hydronium, a weathering exchange.
   Across the world, the acid came and went;
   A single ocean-atmosphere event.

Geology 42 1103

Other geosonnets: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64  65 66

Saturday, January 10, 2015

Geosonnet 24

The linear progressions we assume
sphericalize our precious holy cows
the certainty simplicities presume
breed dreamt-up facts we dutifully espouse
Repeated careful data overthrow
and phosphorus impurities reveal
Olivine is white-hot Devil's snow
A closet skeleton time can't anneal.
This phoenix from volcano is reborn
Forgotten stories texture can unearth
abandon simple models, do not mourn
Complexity's explanatory worth.
   The simple models woo, but cannot stay.
   Eventually the facts get in the way.

Geology 42 867 

Other geosonnets: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64  65 66

Wednesday, December 31, 2014

Blog hiatus

So, I broke my ankle back in October, and after surgery and as a result, work and parenting has sucked up pretty much all of my time. And the geosonnet backlog has finally run its course. Also, although the "moon boot" is marketed as bing for walking, it doesn't seem to be particularly good for walking on lava. I'm guessing it was designed by a non-geologist.