A fossil book

/

We're proud to announce the latest book from Agile Libre. Woot!

I can't take a lot of credit for this book... The idea came from 52 Things stalwart Alex Cullum, a biostratigrapher I met at Statoil in Stavanger in my first proper job. A fellow Brit, he has a profound enthusiasm for all things outside, and for writing and publishing. With able help from Allard Martinius, also a Statoil scientist and a 52 Things author from the Geology book, Alex generously undertook the task of inviting dozens of awesome palaeontologists, biostratigraphers, palynologists, and palaeobotanists from all over the world, and keeping in touch as the essays came in. Kara and I took care of the fiddly bits, and now it's all nearly done. It is super-exciting. Just check out some of the titles:

  • A trace fossil primer by Dirk Knaust
  • Bioastronomy by Simon Conway Morris
  • Ichnology and the minor phyla by S George Pemberton
  • A walk through time by Felix Gradstein
  • Can you catch criminals with pollen? by Julia Webb
  • Quantitative palaeontology by Ben Sloan

It's a pretty mouthwatering selection, even for someone like me who mostly thinks about seismic these days. There are another 46 like this. I can't wait to read them, and I've read them twice already.

Help a micropalaeontologist

The words in these books are a gift from the authors — 48 of them in this book! — to the community. We cherish the privilege of reading them before anyone else, and of putting them out into the world. We hope they reach far and have impact, inspiring people and starting conversations. But we want these books to give back to the community in other ways too, so from each sale we are again donating to a charity. This time it's the Educational Trust of The Micropalaeontological Society. I read about this initiative in a great piece for Geoscientist by Haydon Bailey, one of our authors: Micropalaeontology under threat!. They need our community's support and I'm excited about donating to them.

The book is in the late stages of preparation, and will appear in the flesh in about the middle of November. To make sure you get yours as soon as it's ready, you can pre-order it now.

Pre-order now from Amazon.com 
Save almost 25% off the cover price!
It's $14.58 today, but Amazon sets the final price...

The hack is back: An invitation to get creative

/

We're organizing another hackathon! It's free, and it's for everyone — not just programmers. So mark your calendar for the weekend of 25 and 26 October, sign up with a friend, and come to Denver for the most creative 48 hours you'll spend this year. Then stay for the annual geophysics fest that is the SEG Annual Meeting!

First things first: what is a hackathon? Don't worry, it's not illegal, and it has nothing to do with security. It has to do with ideas and collaborative tool creation. Here's a definition from Wikipedia:

A hackathon (also known as a hack day, hackfest, or codefest) is an event in which computer programmers and others involved in software development, including graphic designers, interface designers and project managers, collaborate intensively on software projects.

I would add that we just need a lot of scientists — you can bring your knowledge of workflows, attributes, wave theory, or rock physics. We need all of that.

Creativity in geophysics

The best thing we can do with our skills — and to acquire new ones — is create things. And if we create things with and alongside others, we learn from them and they learn from us, and we make lasting connections with people. We saw all this last year, when we built several new geophysics apps:

hackathon_2014_calendar.png

The event is at the THRIVE coworking space in downtown Denver, less than 20 minutes' walk from the convention centre — a Manhattan distance of under 1 mile. They are opening up especially for us — so we'll have the place to ourselves. Just us, our laptops, high-speed WiFi, and lots of tacos. 

Sign up here.It's going to be awesome.

The best in the biz

GeoTeric_logo.jpg

This business is blessed with some forward-looking companies that know all about innovation in subsurface geoscience. We're thrilled to have some of them as sponsors of our event, and I hope they will also be providing coders and judges for the event itself. So far we have generous support from dGB — creators of the OpendTect seismic interpretation platform — and ffA — creators the GeoTeric seismic attribute analysis toolbox. A massive Thank You to them both.

If you think your organization might be up for supporting the event, please get in touch! And remember, a fantastic way to support the event — for free! — is just to come along and take part. Sign your team up here!

Student grants

We know there's a lot going on at SEG on this same weekend, and we know it's easier to get money for traditional things like courses. So... We promise that this hackathon will bring you at least as much lasting joy, insight, and skill development as any course. And, if you'll write and tell us what you'd build, we'll consider you for one of four special grants of $250 to help cover your extra costs. No strings. Send your ideas to matt@agilegeoscience.com.

Update

on 2014-09-07 12:17 by Matt Hall

OpenGeoSolutions, the Calgary-based tech company that's carrying the FreeUSP torch and exporing the frequency domain so thoroughly, has sponsred the hackathon again this year. Thank you to Jamie and Chris and everyone else at OGS!

July linkfest

/

It's linkfest time again. All the links, in one handy post.

First up — I've seen some remarkable scientific visualizations recently. For example, giant ocean vortices spiralling across the globe (shame about the rainbow colourbar though). Or the trillion-particle Dark Sky Simulation images we saw at SciPy. Or this wonderful (real, not simulated) video by the Perron Group at MIT:

Staying with visuals, I highly recommend reading anything by Mike Bostock, especially if you're into web technology. The inventor of D3.js, a popular data viz library, here's his exploration of algorithms, from sampling to sorting. It's more conceptual than straight up visualization of data, but no less insightful. 

And I recently read about some visual goodness combined with one of my favourite subjects, openness. Peter Falkingham, a palaeontologist at the Royal Vetinary College and Brown University, has made a collection of 3D photographs of modern tracks and traces available to the world. He knows his data is more impactful when others can use it too.

Derald Smith and sedimentology

From Smith et al. (2009) in SEPM Special Publication No. 97.The geological world was darkened by the death of Derald Smith on 18 June. I met Derald a few times in connection with working on the McMurray Formation of Alberta, Canada during my time at ConocoPhillips. We spent an afternoon examining core and seismic data, and speculating about counter-point-bars, a specialty of his. He was an intuitive sedimentologist whose contributions will be remembered for many years.

Another geological Smith is being celebrated in September at the Geological Society of London's annual William Smith Meeting. The topic this year is The Future of Sequence Stratigraphy: Evolution or Revolution? Honestly, my first thought was "hasn't that conversation been going on since 1994?", but on closer inspection, it promises to be an interesting two days on 'source-to-sink', 'landscape into rock', and some other recent ideas.

The issue of patents reared up in June when Elon Musk of Tesla Motors announced the relaxation of their patents — essentially a promise not to sue anyone using one of their patented technology. He realizes that a world where lots of companies make electric vehicles is better for Tesla. I wrote a piece about patents in our industry.

Technology roundup

A few things that caught our eye online:

Last thing: did you know that the unit of acoustic impedance is the Rayl? Me neither. 

Previous linkfests: April — January — October.

The figure is from Smith et al. (2009), Stratigraphy of counter-point-bar and eddy accretion deposits in low-energy meander belts of the Peace–Athabasca delta, northeast Alberta, Canada. In: SEPM Special Publication No. 97, ISBN 978-1-56576-305-0, p. 143–152. It is copyright of SEPM, and used here in accordance with their terms.

Looking forward to SciPy 2014

/

This week the Agile crew is at the SciPy conference in Austin, Texas. SciPy is a scientific library for the Python programming language, and the eponymous conference is the annual meetup for the physicists, astonomers, economists — and even the geophysicists! — that develop and use SciPy.

What is SciPy?

Python is an awesome high-level programming language. It's awesome because...

  • Python is free and open source.
  • Python is easy to learn and quite versatile.
  • Python has hundreds of great open source extensions, called libraries.
  • The Python ecosystem is actively developed by programmers at Google, Enthought, Continuum, and elsewhere.
  • Python has a huge and talkative user community, so finding help is easy.

All of these factors make it ideal for crunching and visualizing scientific data. The most important of these is NumPy, which provides efficient linear algebra operations — essential for handling big vectors and matrices. SciPy builds on NumPy to provide signal processing, statistics, and optimization. There are other packages in the same ecosystem for plotting, data management, and so on.

If you follow this blog, you know we have been getting into code lately. We think that languages like Python, GNU Octave, and R (a stastical language) are a core competency for geoscientists. That's why we want to help geoscientists learn Python, and why we organize hackathons, and why we keep going on about it on the blog.

What's going on in Austin?

Technical organizers Katy Huff and Serge Rey have put together a fantastic schedule including 2 days of tutorials (already underway), 3 days of technical talks and posters, and 2 days of sprints (focused coding sessions). Interspersed throughout the talk days are 'Birds of a Feather' meetups for various special-interest groups, and more social gatherings. It's exactly what a scientific conference should be: active learning, content, social, hacking, and unstructured discussion.

Here are some of the things I'm most looking forward to:

If you're interested in hearing about what's going on in this corner of the geophysical and scientific computing world, tune in this week to read more. We'll be posting regularly to the blog, or you can follow along on the #SciPy2014 Twitter hashtag.

Have some bacn

/

You might have noticed a lot of emails from Canadian companies recently, asking you to confirm that you wish to receive emails from them. This is because a key part of the 2010 anti-spam law comes into effect tomorrow. We haven't sent you anything, becase we have always complied with the spirit of the law.

What is spam?

We all know what spam is, and the Canadian government's definition is plain:

commercial electronic messages [received] without the recipient's consent

And here's a definition of bacn (pronounced 'bacon') from author Jonathon Keats:

Spam by personal request

This seems to contradict the first definition, but the idea is that bacn is better than spam, but still not as good as a personal email. It's commercial email that you asked for. (Aside: according to that same author, bacn from geologists is quakn.)

Email from Agile*

Because we want you to have as much control over your inbox as possible, I have just switched our email subscription service from Feedburner to MailChimp. One of the reasons is MailChimp's excellent and rigorous anti-spam policy enforcement. Their emails make it very clear who an email is from, and how to unsubscribe from them. 

If you receive our blog updates via email, I hope you see them as a service and not a nuisance. If you're unsure about subscribing because you fear receiving promotions and so on — I promise that all you will ever get is our blog posts. It's just a convenient way to read the blog for some people. 

Just to be clear:

  • We will never add you to a mailing list that you didn't expressly subscribe to.
  • We will always give you an easy way to unsubcribe.
  • We will never share your email address or name with anyone else.
  • We will only send you emails that have an obvious Unsubscribe option.

Other ways to read

Here are some other options for subscribing to our RSS feed, which you will find at /journal/rss.xml 

We want you to be able to easily find, read, interact with, and share our content. If there is some other way we can serve you, please let us know. 

The can of spam image is by Flickr's Clyde Robinson and licensed CC-BY.

Mining innovation

/

by Jelena Markov and Tom Horrocks

Jelena is a postgraduate student and Tom is a research assistant at the University of Western Australia, Perth. They competed in the recent RIIT Unearthed hackathon, and kindly offered to tell us all about it. Thank you, Jelena and Tom!

Two weeks ago Perth coworking space Spacecubed hosted a unique 54-hour-long hackathon focused on the mining industry. Most innovations in the mining industry are the result of long-term strategic planning in big mining companies, or collaboration with university groups. In contrast, the Unearthed hackathon provided different perspectives on problems in the mining domain by giving 'outsiders' a chance to work on industry problems.

The event attracted web-designers, software developers, data gurus, and few geology and geophysics geeks, all of whom worked together on data — both open and proprietary from the Western Australian Government and industry respectively — to deliver time-constrained solutions to problems in the mining domain. There were around 100 competitors divided into 18 teams, but just one underlying question: can web-designers and software developers create solutions that compete, on an innovative level, with those from the R&D divisions of mining companies? Well, according to panel of mining executives and entrepreneurs, they can.

Safe, seamless shutdown

The majority of the teams chose to work on logistic problems in mining production. For example, the Stockphiles worked on a Rio Tinto problem about how to efficiently and safely shut down equipment without majorly disturbing the overall system. Their solution used Directed Acyclic Graphs as the basis for an interactive web-based interface that visualised the impacted parts of the system. Outside of the mining production domain, however, two teams tackled problems focused on geology and geophysics...

Geoscience hacking

The team Ultramafia used augmented reality and cloud-based analysis to visualize geological mapping, with the underlying theme of the smartphone replacing the geological hammer, and also the boring task of joint logging!

The other team in this domain — and the team we were part of — was 50 Grades of Shale...

The team consisted of three PhD students and three staff members from the Centre for Exploration Targeting at the UWA. We created an app for real-time downhole petrophysical data analysis — dubbed Wireline Spelunker — that automatically classifies lithology types from wireline logs and correlates user-selected log segments across the drill holes. We used some public libraries for machine learning and signal analysis algorithms, and within 54 hours the team had implemented a workflow and interface, using data from the government database.

The boulder detection problem

The first prize, a 1 oz gold medal, was awarded to Applied Mathematics, who came up with an extraordinary use of accelerometers. They worked on Rio Tinto's 'boulder detection' problem — early detection of a large rocks loaded into mining trucks in order to prevent crusher malfunctions later in the process, which could ultimately cost $250,000 per hour in lost revenue. The team's solution was to detect large boulders by measuring the truck's vibrations during loading.

Second and third prizes went to Pit IQ and The Froys respectively. Both teams worked on data visualization problems on the mine site, and came up with interactive mobile dashboards.

A new role for Perth?

Besides having a chance to tackle problems that are costing the mining industry millions of dollars a year, this event has demonstrated that Perth is not just a mining hub but also has potential for something else.

This potential is recognized by event organizers Resources Innovation through Information Technology — Zane, Justin, Paul, and Kevin. They see potential in Perth as a centre for tech start-ups focused on the resource industry. Evidently, the potential is huge.

Follow Jelena on Twitter

Free the (seismic) data!

/

Yesterday afternoon Evan and I hosted the second unsession at the GeoConvention in Calgary. After last year exposing 'Free the data' as one of the unsolved problems in subsurface geoscience, we elected to explore this idea further. And we're addicted to this kind of guided, recorded conversation.

Attendance was a little thin, but those who came spent the afternoon deep in conversation about open data, open software, and greater industry transparency. And we unearthed an exciting and potentially epic conclusion that I hope leads to a small revolution.

What happened?

Rather than leaving the floor completely open, we again brought some structure to the proceedings. I'll post the full version to the wiki page, but here's the overview:

  1. Group seismic interpretation: 5 interpreters in 5 minutes.
  2. Stories about openness: which of 26 short stories resonate with you most?
  3. Open/closed, accessible/inaccessible: a scorecard for petroleum geoscience.
  4. Where are the opportunities? What should we move from closed to open?

As you might expect, the last part was the real point. We wanted to find some high-value areas to poke, or at least gather evidence around. And one area—one data type—was identified as being (a) closed and inaccessible in Canada and (b) much more impactful if it were open and accessible. I gave the punchline away in the title, but that data type is seismic data.

Open, public seismic data is much too juicy a topic to do justice to in this post, so stay tuned for a review of some the specifics of how that conversation went. Meanwhile, imagine a world with free, public seismic data...

Reflections on the 2nd edition

The afternoon went well, and the outcome was intriguing, but we were definitely disappointed by the turnout. We have multiple working hypotheses about it...

  • There may not be a strong appetite for this sort of session, especially on a 'soft' topic. Next time: seismic resolution?
  • The first day might not be the best time for it, because people are still in the mood for talks. Next time: Wednesday morning?
  • The programme maybe didn't reflect what the unsession was about, and the time was unclear. Next time: More visibility.
  • Three hours may be too much to ask from people, though you could say the same about any other session here.

We'd love to hear your thoughts too... Are we barking up completely the wrong tree? Does our community even want to have these conversations? Should we try again in 2015?

April linkfest

/

It's time for our regular linkfest!

There's a new book in town... Rob Simm and Mike Bacon have put together a great-looking text on seismic amplitude intepretation (Cambridge, 2014). Mine hasn't arrived yet, so I can't say much more — for now, you can preview it in Google Books. I should add it to my list.

Staying with new literature, I started editing a new column in SEG's magazine The Leading Edge in February. I wrote about the first instalment, and now the second is out, courtesy of Leo Uieda — check out his tutorial on Euler deconvolution, complete with code. Next up is Evan with a look at synthetics.

On a related note, Matteo Niccoli just put up a great blog post on his awesome perceptual colourmaps, showing how to port them to matplotlib, the MATLAB-like plotting environment lots of people use with the Python programming language. 

Dolf Seilacher, the German ichnologist and palaeontologist, died 4 days ago at the age of 89. For me at least, his name is associated with the mysterious trace fossil Palaeodictyon — easily one of the weirdest things on earth (right). 

Geoscience mysteries just got a little easier to solve. As I mentioned the other day, there's a new place on the Internet for geoscientists to ask questions and help each other out. Stack Exchange, the epic Q&A site, has a new Earth Science site — check out this tricky question about hydrocarbon generation.

And finally, who would have thought that waiting 13 years for a drop of bitumen could be an anticlimax? But in the end, the long (if not eagerly) awaited 9th drop in the University of Queensland's epic experiment just didn't have far enough to fall...

If you can't get enough of this, you can wait for the 10th drop here. Or check back here in 2027.

A culture of asking questions

/

When I worked at ConocoPhillips, I was quite involved in their knowledge sharing efforts (and I still am). The most important part of the online component is a set of 100 or so open discussion forums. These are much like the ones you find all over the Internet (indeed, they're a big part of what made the Internet what it is — many of us remember Usenet, now Google Groups). But they're better because they're highly relevant, well moderated, and free of trolls. They are an important part of an 'asking' culture, which is an essential prerequisite for a learning organization. 

Stack Exchange is awesome

Today, the Q&A site I use most is Stack Overflow. I read something on it almost every day. This is the place to get questions about programming answered fast. It is one of over 100 sites at Stack Exchange, all excellent — readers might especially like the GIS Stack Exchange. These are not your normal forums... Fields medallist Tim Gowers recognizes Math Overflow as an important research tool. The guy has a blog. He is awesome.

What's so great about the Stack Exchange family? A few things:

  • A simple system of up- and down-voting questions and answers that ensures good ones are easy to find.
  • A transparent system of user reputation that reflects engagement and expertise, and is not easy to game. 
  • A well defined path from proposal, to garnering support, to private testing, to public testing, to launch.
  • Like good waiters, the moderators keep a very low profile. I rarely notice them. 
  • There are lots of people there! This always helps.

The new site for earth science

The exciting news is that, two years after being proposed in Area 51, the Earth Science site has reached the minimum commitment, spent a week in beta, and is now open to all. What happens next is up to us — the community of geoscientists that want a well-run, well-populated place to ask and answer scientific questions.

You can sign in instantly with your Google or Facebook credentials. So go and take a look... Then take a deep breath and help someone. 

More AAPG highlights

/

Here are some of our highlights from the second half of the AAPG Annual Convention in Houston.

Conceptual uncertainty in interpretation

Fold-thrust belt, offshore Nigeria. Virtual Seismic Atlas.Rob Butler's research is concerned with the kinematic evolution of mountain ranges and fold thrust belts in order to understand the localization of deformation across many scales. Patterns of deformed rocks aren't adequately explained by stress fields alone; they are also controlled by the mechancial properties of the layers themselves. Given this fact, the definition of the layers becomes a doubly important part of the interpretation.

The biggest risk in structural interpretation is not geometrical accuracy but whether or not the concept is correct. This is not to say that we don't understand geologic processes. Rather, a section can always be described in more than one way. It is this risk in the first order model that impacts everything we do. To deal with conceptual uncertainty we must first capture the range, otherwise it is useless to do any more refinement. 

He showed a crowd-sourced compiliation of 24 interpretations from the Virtual Seismic Atlas as a way to stack up a series of possible structural frameworks. Fifteen out of twenty-four interviewees interpreted a continuous, forward-propagating thrust fault as the main structure. The disagreements were around the existence and location of a back thrust, linkage between fore- and back-thrusts, the existence and location of a detachment surface, and its linkage to the fault planes above. Given such complexity, "it's rather daft," he said, "to get an interpretation from only one or two people." 

CT scanning gravity flows

Mike Tilston and Bill Arnott gave a pair of talks about their research into sediment gravity flows in the lab. This wouldn't be newsworthy in itself, but their 2 key innovations caught our attention: 

  1. A 3D velocity profiler capable of making 23 measurements a second
  2. The flume tank ran through a CT scanner, giving a hi-res cross-section view

These two methods sidestep the two major problems with even low-density (say 4% by weight) sediment gravity flows: they are acoustically attenuative, and optically opaque. Using this approach Tilston and Arnott investigated the effect of grain size on the internal grain distribution, finding that fine-grained turbidity currents sustain a plug-like wall of sediment, while coarse-grained flows have a more carpet-like distribution. Next, they plan to look at particle shape effects, finer grain sizes, and grain mixtures. Technology for the win!

Hypothesizing a martian ocean

Lorena Moscardelli showed topograhic renderings of the Eberswalde delta (right) on the planet Mars, hypothesizing that some martian sedimentary rocks have been deposited by fluvial processes. An assertion that posits the red planet with a watery past. If there are sedimentary rocks formed by fluids, one of the fluids could have been water. If there has been water, who knows what else? Hydrocarbons? Imagine that! Her talk was in the afternoon session on Space and Energy Frontiers, sandwiched by less scientific speakers raising issues for staking claims and models for governing mineral and energy resources away from earth. The idea of tweaking earthly policies and state regulations to manage resources on other planets, somehow doesn't align with my vision of an advanced civilization. But the idea of doing seismic on other planets? So cool.

Poster gorgeousness

Matt and I were both invigorated by the quality, not to mention the giant size, of the posters at the back of the exhibition hall. It was a place for the hardcore geoscientists to retreat from the bright lights, uniformed sales reps, and the my-carpet-is-cushier-than-your-carpet marketing festival. An oasis of authentic geoscience and applied research.

We both finally got to meet Brian Romans, a sedimentologist at Virginia Tech, amidst the poster-paneled walls. He said that this is his 10th year venturing to the channel deposits that crop out in the Magallanes Basin of southern Chile. He is now one of the three young, energetic profs behind the hugely popular Chile Slope Systems consortium.

Three years ago he joined forces with Lisa Stright (University of Utah), and Steve Hubbard (University of Calgary) and formed the project investigating processes of sediment transfer across deepwater slopes exposed around Patagonia. It is a powerhouse of collaborative research, and the quality of graduate student work being pumped out is fantastic. Purposeful and intentional investigations carried out by passionate and tech-savvy scientists. What can be more exciting than that?

Do you have any highlights of your own? Please leave a note in the comments.