Reproduce this!

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There’s a saying in programming: untested code is broken code. Is unreproducible science broken science?

I hope not, because geophysical research is — in general — not reproducible. In other words, we have no way of checking the results. Some of it, hopefully not a lot of it, could be broken. We have no way of knowing.

Next week, at the SEG Annual Meeting, we plan to change that. Well, start changing it… it’s going to take a while to get to all of it. For now we’ll be content with starting.

We’re going to make geophysical research reproducible again!

Welcome to the Repro Zoo!

If you’re coming to SEG in Anaheim next week, you are hereby invited to join us in Exposition Hall A, Booth #749.

We’ll be finding papers and figures to reproduce, equations to implement, and data tables to digitize. We’ll be hunting down datasets, recreating plots, and dissecting derivations. All of it will be done in the open, and all the results will be public and free for the community to use.

You can help

There are thousands of unreproducible papers in the geophysical literature, so we are going to need your help. If you’ll be in Anaheim, and even if you’re not, here some things you can do:

That’s all there is to it! Whether you’re a coder or an interpreter, whether you have half an hour or half a day, come along to the Repro Zoo and we’ll get you started.

Figure 1 from Connolly’s classic paper on elastic impedance. This is the kind of thing we’ll be reproducing.

Figure 1 from Connolly’s classic paper on elastic impedance. This is the kind of thing we’ll be reproducing.

Unsolved problems in applied geoscience

I like unsolved problems. I first wrote about them way back in late 2010 — Unsolved problems was the eleventh post on this blog. I touched on the theme again in 2013, before and after the first 'unsession' at the GeoConvention, which itself was dedicated to finding the most pressing questions in exploration geoscience. As we turn towards the unsession at AAPG in Salt Lake City in May, I find myself thinking again about unsolved problems. Specifically, what are they? How can we find them? And what can we do to make them easier to solve?

It turns out lots of people have asked these questions before.

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I've compiled a list of various attempts by geoscientists to list he big questions in the field. The only one I was previous aware of was Milo Backus's challenges in applied seismic geophysics, laid out in his president's column in GEOPHYSICS in 1980 and highlighted later by Larry Lines as part of the SEG's 75th anniversary. Here are some notable attempts:

  • John William Dawson, 1883 — Nova Scotia's most famous geologist listed unsolved problems in geology in his presidential address to the American Association for the Advancement of Science. They included the Cambrian Explosion, and the origin of the Antarctic icecap. 
  • Leason Heberling Adams, 1947 — One of the first experimental rock physicists, Adams made the first list I can find in geophysics, which was less than 30 years old at the time. He included the origin of the geomagnetic field, and the temperature of the earth's interior.
  • Milo Backus, 1980 — The list included direct hydrocarbon detection, seismic imaging, attenuation, and anisotropy.  
  • Mary Lou Zoback, 2000 — As her presidential address to the GSA, Zoback kept things quite high-level, asking questions about finding signal indynamic systems, defining mass flux and energy balance, identifying feedback loops, and communicating uncertainty and risk. This last one pops up in almost every list since.
  • Calgary's geoscience community, 2013 — The 2013 unsession unearthed a list of questions from about 50 geoscientists. They included: open data, improving seismic resolution, dealing with error and uncertainty, and global water management.
  • Daniel Garcia-Castellanos, 2014 — The Retos Terrícolas blog listed 49 problems in 7 categories, ranging from the early solar system to the earth's interior, plate tectonics, oceans, and climate. The list is still maintained by Daniel and pops up occasionally on other blogs and on Wikipedia.

The list continues — you can see them all in this presentation I made for a talk (online) at the Bureau of Economic Geology last week (thank you to Sergey Fomel for hosting me!). During the talk, I took the opportunity to ask those present what their unsolved problems are, especially the ones in their own fields. Here are a few of what we got (the rest are in the preso):

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What are your unsolved problems in applied geoscience? Share them in the comments!


If you have about 50 minutes to spare, you can watch the talk here, courtesy of BEG's streaming service.

Click here to watch the talk >>>

Must-read geophysics

If you had to choose your three favourite, most revisited, best remembered papers in all of exploration geophysics, what would you choose? Are they short? Long? Full of math? Well illustrated? 

Keep it honest

Barnes, A (2007). Redundant and useless seismic attributes. Geophysics 72 (3). DOI:10.1190/1.2716717
Rarely do we see engaging papers, but they do crop up occasionally. I love Art Barnes's Redundant and useless seismic attributes paper. In this business, I sometimes feel like our opinions — at least our public ones — have been worn down by secrecy and marketing. So Barnes's directness is doubly refreshing:

There are too many duplicate attributes, too many attributes with obscure meaning, and too many unstable and unreliable attributes. This surfeit breeds confusion and makes it hard to apply seismic attributes effectively. You do not need them all.

And keep it honest

Blau, L (1936). Black magic in geophysical prospecting. Geophysics 1 (1). DOI:10.1190/1.1437076
I can't resist Ludwig Blau's wonderful Black magic geophysics, published 77 years ago this month in the very first issue of Geophysics. The language is a little dated, and the technology mostly sounds rather creaky, but the point, like Blau's wit, is as fresh as ever. You might not learn a lot of geophysics from this paper, but it's an enlightening history lesson, and a study in engaging writing the likes of which we rarely see in Geophysics today...

And also keep it honest

Bond, C, A Gibbs, Z Shipton, and S Jones (2007), What do you think this is? "Conceptual uncertainty" in geoscience interpretation. GSA Today 17 (11), DOI: 10.1130/GSAT01711A.1
I like to remind myself that interpreters are subjective and biased. I think we have to recognize this to get better at it. There was a wonderful reaction on Twitter yesterday to a recent photo from Mars Curiosity (right) — a volcanologist thought it looked like a basalt, while a generalist thought it more like a sandstone. This terrific paper by Clare Bond and others will help you remember your biases!

My full list is right here. I hope you think there's something missing... please edit the wiki, or put your personal favourites in the comments. 

The attribute figure is adapted from from Barnes (2007) is copyright of SEG. It may only be used in accordance with their Permissions guidelines. The Mars Curiosity figure is public domain. 

Species identification in the rock kingdom

Like geology, life is studied across a range of scales. Plants and animals come in a bewildering diversity of shapes and sizes. Insects can be microscopic, like fleas, or massive, like horned beetles; redwood trees tower 100 metres tall, and miniature alpine plants fit into a thimble.

In biology, there is an underlying dynamic operating on all organisms that constrain the dimensions and mass of each species. These constraints, or allometric scaling laws, play out everywhere on earth because of the nature and physics of water molecules. The surface tension of water governs the strength of a cell wall, and this in turn mandates the maximum height and width of a body, any possible body.

← The relationship between an organisms size and mass. Click the image to read Kevin Kelly's fascinating take on this subject.

Amazingly, both animal and plant life forms adhere to a steady slope of mass per unit length. Life, rather than being boundless and unlimited in every direction, is bounded and limited in many directions by the nature of matter itself. A few things caught my attention when I saw this graph. If your eye is keenly tuned, you'll see that plants plot in a slightly different space than animals, with the exception of only a few outliers that cause overlap. Even in the elegantly constructed world of the biological kingdom, there are deviations from nature's constraints. Scientists looking at raw data like these might certainly describe the outliers as "noise", but I don't think that's correct in this case; it's just undescribed signal. If this graphical view of the biological kingdom is used as a species identifcation challenge, sometimes a plant can 'look' like an animal, but it really isn't. It's a plant. A type II error may be lurking.

Finally, notice the wishbone pattern in the data. It's reminded me of some Castagna-like trends I have come across in the physics of rocks, and I wonder if this suggests a common end-member source of some kind. I won't dare to elaborate on these patterns in the animal kingdom or plant kingdom, but it's what I strive for in the rock kingdom.

I wonder if this example can serve as an analog for many rock physics relationships, whereby the fundamental properties are governed by some basic building blocks. Life forms have carbon and DNA as their common roots, whereas sedimentary rocks don't necessarily have ubiquitous building blocks; some rocks can be rich in silica, some rocks can have none at all. 

← Gardner's equation: the relationship between acoustic velocity and bulk density for sedimentary rocks. Redrawn from Gardner et al (1974).

For comparison, look at this classic figure from Gardner et al in which they deduced an empirical relationship between seismic P-wave velocity and bulk density. As in the first example, believing that all species fall on this one global average (dotted line) is cursory at best. But, that is exactly what Gardner's equation describes. In fact, it fits more closely to high-velocity dolomites than it does for the sands and silts for which it is typically applied. Here, I think we are seeing the constraints from water impose themselves differently on the formation of different minerals, and depositional elements. Deviations from the global average are meaningful, and density estimation and log editing techniques should (and usually do) take these shifts into account. Even though this figure doesn't have any hard data on it, I am sure you could imagine that, just as with biology, crossovers and clustering would obscure these relatively linear deductions.

← The mudrock line: relationship between shear velocity and compressional velocitiy, modfified from Castagna et al (1985).

The divergence of mudrocks from gas sands that John Castagna et al discovered seems strikingly similar to the divergence seen between plant and animal cells. Even the trend lines suggest a common or indistinguishable end member. Certainly the density and local kinetic energy of moving water has alot to do with the deposition and architecture of sediment bodies. The chemical and physical properties of water affect sediments undergoing burial and compaction, control diagensis, and control pore-fluid interactions. Just as water is the underlying force causing the convergence in biology, water is one (and perhaps not the only) driving force that constrains the physical properties of sedimentary rocks. Any attempts at regression and cluster analyses should be approached with these observations in mind.

References

Kelly, K (2010). What Technology Wants. New York, Viking Penguin.

Gardner, G, L Gardner and A Gregory (1974). Formation velocity and density—the diagnostic basics for stratigraphic traps. Geophysics 39, 770–780.

Castagna, J, M Batzle and R Eastwood (1985). Relationships between compressional-wave and shear-wave velocities in clastic silicate rocks. Geophysics 50, 571–581.

What's hot in geophysics?

Two weeks ago I visited Long Beach, California, attending a conference called Mathematical and Computational Issues in the Geosciences, organized by the Society of Industrial and Applied Mathematicians. I wanted to exercise my cross-thinking skills. 

As expected, the week was very educational for me. Well, some of it was. Some of it was like being beaten about the head with a big bag of math. Anyone for quasi-monotone advection? What about semi-implicit, semi-Lagrangian, P-adaptive discontinuous Galerkin methods then?

Notwithstanding my apparent learning disability, I heard about some fascinating new things. Here are three highlights.

Read More

The etiology of rivers

The Ordovician was a primitive time. No mammals. No birds. No flowers. Most geologists know this, right? How about this: No meandering rivers.

Recently several geo-bloggers wrote about geological surprises. This was on my shortlist. 

A couple of weeks ago, Evan posted the story of scale-free gravity deformation we heard from Adrian Park and his collaborators at the Atlantic Geological Society's annual Colloquium. My own favourite from the conference was Neil Davies' account of the evolution of river systems:

Davies, Neil & Martin Gibling (2011). Pennsylvanian emergence of anabranching fluvial deposits: the parallel rise of arborescent vegetation and fixed-channel floodplains.

Neil, a post-doctoral researcher at Dalhousie University in Nova Scotia, Canada, started with a literature review. He read dozens of case studies of fluvial geology from all over the world, noting the interpretation of river morphology (fluvotype?). What he found was, to me at least, surprising: there were no reported meandering rivers before the Devonian, and no anabranching rivers before the Carboniferous. 

The idea that rivers have evolved over time, becoming more diverse and complex, is fascinating. At first glance, rivers might seem to be independent of life and other manifestly time-bound phenomena. But if we have learned only one thing in the last couple of decades, it is that the earth's systems are much more intimately related than this, and that life leaves its fingerprint on everything on earth's surface. 

A little terminology: anastomosing, a term I was more familiar with, is not strictly the correct term for these many-branched, fixed-channel rivers. Sedimentologists prefers anabranching. Braided and meandering river types are perhaps more familiar. The fluviotypes I'm showing here might be thought of as end members — most rivers show all of these characteristics through time and space.

What is the cause of this evolution? Davies and Gibling discussed two parallel effects: bank stabilization by soil and roots, and river diversion, technically called avulsion, by fallen trees. The first idea is straightforward: plants colonize river banks and floodplains, thus changing their susceptibility to erosion. The second idea was new to me, but is also simple: as trees got taller, it became more and more likely that fallen trunks would, with time, make avulsion more likely. 

There is another river type we are familiar with in Canada: the string of beaver dams (like this example from near Fort McMurray, Alberta). I don't know for sure, but I bet these first appeared in the Eocene. I have heard that the beaver is second only to man in terms of the magnitude of its effect on the environment. As usual, I suspect that microbes were not considered in this assertion.

All of this makes me wonder: are there other examples of evolution expressing itself in geomorphology like this?

Many thanks to Neil and Martin for allowing us to share this story. Please forgive my deliberate vagueness with some of the details — this work is not yet published; I will post a link to their forthcoming paper when it is published. The science and the data are theirs, any errors or inconsistencies are mine alone.