Sunday, August 31, 2014

Friday, August 29, 2014

Geology sonnet roundup

Firstly, I would like to place all six science week sonnets (plus the bonus poem) in stratigraphic order.  That is, youngest rocks described at the top. An analysis will follow the poetry:


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.

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

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?

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.

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.

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.

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.

Thus ends what is possibly the least effective science awareness effort ever. I made it.  A sonnet a day, pulled from the pages of Geology, for the last 6 days of Science Week. And a bonus one earlier today, to try out some ideas I had while thinking up this post. If I wanted to kid myself, I would say that my failure was that I picked something too popular, and that the sonnets got lost in the celebrity gossip and other pop culture frivolity that haunts this form on the internet.  If only I had gone for American Mineralogist Villanelles.

This is not an entirely honest assessment. It was a tricky brief.  For the first few sonnets (1, 2, 4), I was basically seeing how well or badly I could jam technical terms and concepts into the structure without irreparably breaking the sonnet form, and still extracting the basic gist of the paper.  With 3 and 6, I was trying to show what it was about the study that was really clever- trying to channel the scientific genius in verse, with less of an emphasis on the story or terminology.  And with 5, I was aiming to show the difficulty in getting any data at all for that system, and emphasizing the blood, sweat, and tear aspect of research. Still, there are some core issues relating to good poetry and science writing which remain unresolved.

Others have written at length on the place of metaphor in science writing.   Personally, I think that it can be dangerous, and easily done misleadingly. Science is more like a murder mystery than an allegory. The particulars of who knows what when and how they determine it are generally more important than the anthropomorphisation of the interpretation of the day, but that isn’t always easy to put in verse. 

On the other hand, poetry without metaphor ain’t all that. It is worth at least linking Poe’s Sonnet to Science, which kind of set the mold of science as imagination-killing dreariness.  But the thing that he never realized, is that the universe is stranger and more bizarre than our imaginations.  So it is worth at least trying to convey the breadth and depth of a natural world which is stranger and more wonderful than anything we can possibly imagine without studying it, and then let our feeble human brains decorate those secrets which our scientific labour finally pries from the Earth. Furthermore, most poetry these days doesn’t really aim for accessibility or exposition.  So for 7, I maxxed the metaphor and theme, and didn’t even try to explain.

Overall, it was a fun exercise, and the overwhelming density of explanatory prose evident in the 3QD metrics makes me glad I tried, even if it was too obtuse and catless to interest much of the internet.

Geosonnet 7

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.



Wednesday, August 27, 2014

3QD blogging contest metadata

The long-lived, old-school blogging site 3 quarks daily is holding its annual science blogging contest  They have nominated eighty-five blog posts upon which one can vote to advance it into the finals round.  In theory, this means that everyone voting should read all 85 posts, and make an honest choice.  If that doesn't work, then they should at least skim each post- OK, how about simply clicking the links and glancing at them?

Having done the latter, I doubt more than a few percent of the people who actually vote will do the former.  Because, in addition to clinking the links, I have gone the extra mile micron and extracted their metadata.  And this is how I’m pretty sure not many people are going to read all 85 entries this week- they total over 128,000 words, more than a hefty novel, or two skinny ones. I will summarize it here, for potential voters who want to pretend to be voting knowledgeably, but are too lazy even to look at text summaries.

With the exception of a song (complete with ukulele chords) and a dialogue, the nominated blog posts are all expository prose.  Most of them are written in a serious tone, although there is a smattering of snark, cutsiness, and metaphor. One is written in Spanish, the rest are in English.

Figure 1.  The log of science post length, showing a high end tail.

The length distribution of the nominated blog posts is not normal.  In fact, it is not even log normal (figure 1), as there is a surplus of nominees in excess of 2000 words and/or a deficit of nominees less than 700 words (incidentally, that is the length of a standard print newspaper column). The lengths range from just over 300 words (the song) to just shy of 5000 words, with a mean of about 1200 and a median of about 1500.

  
All but seven of the entries are illustrated. Nine have imbedded video, sixteen list references, two have data tables. Seven entries feature text grabs- featuring (machine unreadable) text presented in image format.  The type of text presented this way varies widely, spanning twitter screengrabs to scanned informal handwriting to page captures of ancient books.

The relationship between the number of images and the number of words is not clear.  I have (arbitrarily) divided the posts up into two groups (figure 2). A small, highly illustrated group, in which the number of illustrations scales with the length of the post, and a main, less illustrated group, where the number of illustrations is essentially unrelated to text length. In the highly illustrated group, there is about one additional figure per 400 words, but the zero word intercept is still quite high- six.

Figure 2. Post length vs. number of imbedded images (embedded text excluded). Groupings are done via eyeball, not statistics.

Hopefully this summary will inform your choices of which articles to read and consider.  Please don’t make any voting choices solely on the metadata.  You are, after all, a human, and not a Facebook algorithm. And sure, if you want to nominate this post for the 2015 contest, I won’t stop you.

A summary table is below:

site
title
words
images
video
text grabs
references (1=present)
table
 3 Quarks Daily
 The Dictionary is not Literature
2539
1




 Action Science Theater
 How to fall and miss the ground
541
4
1



 Aeon
 Cows Might Fly
3473
1




 American Science
 The Curious History of the Paleo-Diet, and its Relationship to Science & Modernity
2194
3




 An Evolutionist's Perspective
 The Woes of Capitalism:  Kinship, Sociality and Economy
1433
0




 Ars Technica
 Could dark matter be hiding in plain sight in existing experiments?
1085
1




 Babies Learning Language
 Shifting our cultural understanding of replication
3158
0




 BBC
 The quest to save the Hollywood bison
1443
4




 Beach Chair Scientist
 Mother Nature vs  Santa Claus
711
0
1
4


 Brainwaves
 Searching For The Elephant’s Genius Inside the Largest Brain on Land
1502
1




 Charismatic Minifauna
 Bats have sparkly poop
606
4




 Chemically Cultured
 That love-hate supervisor relationship
411
0

12


 Cocktail Party Physics
 Seen and Unseen:  Could There Ever Be a “Cinema Without Cuts”?
2400
2
4

1

 Comparatively Psyched
 The Robin's Song
1302
2


1

 Curious Meerkat
 Eating Insects
1827
3
1


1
 Eat Your Brains Out
 Science and the Supernatural
3802
4

1


 Ecology & Evolution
 And to the victor the spoiled
474
1




 Ecology & Evolution
 The Heat and Light of Science Communication
1045
1


1

 Ecology & Evolution
 The Science of Scientific Whaling
1207
2




 Ecology & Evolution
 What is(n’t) palaeontology like?
884
2




 Ecology & Evolution
 What’s it like to study Zoology?
896
1




 Errant Science
 Tradition, in Science
767
2

1


 Eruptions
 So, You Think Yellowstone Is About to Erupt
1295
1




 Genotopia
 Hail Britannia! (Dorkins Reviews Wade)
1759
1




 Genotopia
 On city life, the history of science, and the genetics of race
2298
3




 Grrlscientist
 Influenza:  How the Great War helped create the greatest pandemic ever known
2088
4


1

 Hawkmoth
 On Wildness
494
9




 Huffpost
 A Few Short Rules on Being Creative
1313
1




 Illumination
 GMO Leukemia Outbreak in China
471
1

4


 Inkfish
 Scientists Ask Why There Are So Many Freaking Huge Ants
913
1




 Leaving Plato's Cave
 The Meta-lympics:  a catalyst for scientific discovery
1076
4




 Limulus
 Living Fossils
771
8

8


 Napoli Unplugged
 Procida:  Picture Perfect
881
12




 Napoli Unplugged
 Vesuvius at Night
897
4




 Nautilus
 The Math Trick Behind MP3s, JPEGs, and Homer Simpson’s Face
1599
5




 Neurobabble
 Parasitic wasps vs.  zombie cockroaches
785
1




 Neurobabble
 Technology and the adolescent brain
1112
1




 Neurobabble
 What sign languages have taught us about our brains
1198
2
2



 Nothing in Biology Makes Sense
 When the going gets tough, mutualism gets going
885
3
1

1

 Pacific Standard
 Your Genome Is a Post-Apocalyptic Wasteland
782
1




 Patrick F
 Clarkin, PhD:  Developmental Plasticity and the “Hard-Wired” Problem
4343
3


1

 Pen Sapiens
 Monkey See, Monkey Yawn
764
1


1

 Peter Pearsal
 A Desert Orogeny
995
5




 Planetizen
 The Wicked Problem of Urban Biodiversity, pt 1
897
0




 Psychology Today
 Love, Love Medulla:  The Neuroscience of Beatlemania
1181
6


1

 Preposterous Universe
 How Quantum Field Theory Becomes “Effective”
3553
5




 Preposterous Universe
 Why the Many-Worlds Formulation of Quantum Mechanics Is Probably Correct
2525
2




 Prophage
 Modest Data Reported From Oxford Nanopore's Exciting MinION Sequencing Platform
724
2


1

 Scicurious
 Addiction showcases the brain's flexibility
1086
1




 Science Explained
 Knock, Knock Who’s there?
423
4




 Science Sushi
 Did Allergies Evolve To Save Your Life?
1925
3


1

 Science Sushi
 Muscles Love Oxytocin:  So-Called “Hug Hormone” Important In Muscle Regeneration
767
1


1

 Sexual Selection and Life History Evolution
 Aesthetics, mathematics, physics and biology
1255
3




 Skulls in the Stars
 How *do* cats land on their feet when falling, anyway?
2336
14




 Slate
 Promiscuity Is Pragmatic
1054
3




 Space
 Hazard, Risk, and the Steelhead (Oso) Landslide in Washington
1099
8




 Space
 Real Atmospheric Science in Stargate:  Atlantis
1696
9




 Starts With A Bang
 22 Messages of Hope (and Science) for Creationists
1555
14




 Starts With A Bang
 How is the Universe bigger than its age?
1488
11
1



 Stuff About Space
 The Strangest Star:  A Neutron Star Inside a Red Giant
1021
2




 Synthetic Daisies
 Playing the Long Game of Human Biological Variation
1021
6


1

 Synthetic Daisies
 The game of evolution
3507
17


1
2
 The Bleeding Edge
 Butterflies
2252
1




 The Book of Science
 Photosynthesis
355
0




 The Conversation
 Despite metamorphosis, moths hold on to memories from their days as a caterpillar
988
4




 The Conversation
 The ancient Greek riddle that helps us understand modern disease threats
902
1




 The Conversation
 Why cold-blooded animals don’t need to wrap up to keep warm
608
1




 The Last Word On Nothing
 What Luis Alvarez Did
1654
2




 The Loom
 The Wisdom of (Little) Crowds
1726
1




 The Mermaid's Tale
 Are bees intelligent?
1416
2
1



 The Mermaid's Tale
 The visible colors and the falseness of human races as natural categories
2479
2




 The Mermaid's Tale
 Whooza good gurrrrrl? Whoozmai bayyyy-bee boy?
1839
10

1


 The Neurocritic
 Existential Neuroscience:  a field in search of meaning
1838
5


1

 The Neurocritic
 When Waking Up Becomes the Nightmare:  Hypnopompic Hallucinatory Pain
1161
5


1

 The New Yorker
 The Power of the Hoodie-Wearing C.E.O.
1267
1




 The Philosopher's Beard
 Love's Labours Lost:  How Robots Will Transform Human Intimacy
4822
2




 The Trenches of Discovery
 The human machine:  obsolete components
2572
4




 Things We Don't Know
 Squid Lady Parts
1350
5


1

 Too Long For Twitter
 New neuroscience on why we dream
3052
2




 Tree Town Chemistry
 How One Scientist Broke in to Professional Craft Brewing
847
1




 Unthink
 Five Things Scientists Know About Romance
913
0




 Weekend Adventure
 The Wild Inside
1298
5




 Wired
 Have We Been Interpreting Quantum Mechanics Wrong This Whole Time?
3328
5
1



 Wired
 What is brain death?
1603
1




 You've Got Some Science On You
 Infection:  It's all a matter of perspective
973
2












Total

128775
283
13
31
16
3
mean

1515
3.33
1.4
4.4
1
1.5
median

1207
2


1
1.5