A European geo-gaming hackathon

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I'm convinced that hackathons are the best way to get geoscientists and engineers inventing and collaborating in new ways. They are better for learning than courses. They are better for networking than parties. And they nearly always have tacos! 

If you are unsure what a hackathon is, or why I'm so enthusiastic about them, you can read my November article in the Recorder (Hall 2015, CSEG Recorder, vol 40, no 9).

The next hackathon will be 28 and 29 May in Vienna, Austria — right before the EAGE Conference and Exhibition. You can sign up right now! Please get it in your calendar and pass it along.

Throwing down the gauntlet

Colorado School of Mines has dominated the student showing at the last 2 autumn hackathons. I know there are plenty more creative research groups out there. Come out and show the world your awesomeness — in teams of up to 4 people — and spend a weekend learning and coding. Also: there will be beer.

To everyone else: this is not a student event, it's for everyone. Most of the participants in the past have been professionals, but the more diverse it is, the more we all get out of it. So don't ask yourself if you'll fit in — you will. 

A word about the fee

Our previous hackathons have been free, but this one has a small fee. It's an experiment. Like most free events, no-shows are a challenge; I'm hoping the fee reduces the problem. If the fee makes it difficult for you to join us, please get in touch — I do not want it to be a barrier.

Just to be clear: these events do not make money. Previous events have been generously sponsored — and that's the only way they can happen. We need support for this one too: if you're a champion of creativity in science and want to support this event, you can find me at matt@agilegeoscience.com, or you can read more about sponsorship here.

Details

The dates are 28 and 29 May. The event will run 8 till 6 (or so) on both the Saturday and the Sunday. We don't have a venue finalized yet. Ideas and contributions of any kind are welcome — this is a community event.

The theme this year will be Games. If you have ideas, share them in the comments! Here are some random project ideas to get you going...

  • Acquisition optimizer: lay out the best geometry to image the geology.
  • Human inversion: add geological layers to match a seismic trace.
  • Drill wells on a budget to make the optimal map of an unseen surface.
  • Which geological section matches the (noisy) seismic section?
  • Top Trumps for global 3D seismic surveys, with data scraped from press releases.
  • Set up the best processing flow based for a modeled, noisy shot gather.

It's going to be fun! If you're traveling to EAGE this year, I hope we see you there!

Photo of Vienna by Nic Piégsa, CC-BY. Photo of bridge by Dragan Brankovic, CC-BY.

Old skool plot tool

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It's not very glamorous, but sometimes you just want to plot a SEG-Y file. That's why we crafted seisplot. OK, that's why we cobbled seisplot together out of various scripts and functions we had lying around, after a couple of years of blog posts and Leading Edge tutorials and the like.

Pupils of the old skool — when everyone knew how to write a bash script, pencil crayons and lead-filled beanbags ruled the desktop, and Carpal Tunnel Syndrome was just the opening act to the Beastie Boys — will enjoy seisplot. For a start, it's command line only: 

    python seisplot.py -R -c config.py ~/segy_files -o ~/plots

Isn't that... reassuring? In this age of iOS and Android and Oculus Rift... there's still the command line interface.

Features galore

So what sort of features can you look forward to? Other than all the usual things you've come to expect of subsurface software, like a complete lack of support or documentation. (LOL, I'm kidding.) Only these awesome selling points:

  • Make wiggle traces or variable density plots... or don't choose — do both!
  • If you want, the script will descend into subdirectories and make plots for every SEG-Y file it finds.
  • There are plenty of colourmaps to choose from, or if you're insane you can make your own.
  • You can make PNGs, JPGs, SVGs or PDFs. But not CGM, sorry about that.

Well, I say 'selling points', but the tool is 100% free. We think this is a fair price. It's also open source of course, so please — seriously, please — improve the source code, then share it with the world! The code is in GitHub, natch.

Never go full throwback

There is one more feature: you can go full throwback and add scribbles and coffee stains. Here's one for your wall:

The 2D seismic line in this post is from the USGS NPRA Seismic Data Archive, and are in the public domain. This is line number 31-81-PR (links directly to SEG-Y file).

Rockin' Around The Christmas Tree

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I expect you know at least one geoscientist. Maybe you are one. Or you want to be one. Or you want one for Christmas. It doesn't matter. The point is, it'll soon be Christmas. If you're going to buy someone a present, you might as well get them something cool. So here's some cool stuff!

Gadgets

There isn't a single geologist alive that wouldn't think this was awesome. It's a freaking Geiger counter! It goes in your pocket! It only costs USD 60, or CAD 75, or less than 40 quid! Absurd: these things normally cost a lot more.

OK, if you didn't like that, you're not going to like this IR spectrometer. Yes, a pocket molecular sensor, for sensing molecules in pockets. It does cost USD 250 though, so make sure you really like that geologist!

Back down to earth, a little USB microscope ticks most of the geogeek boxes. This one looks awesome, and is only USD 40 but there are loads, so maybe do some research.

Specimens

You're going to need something to wave all that gadgetry at. If you go down the well-worn path of the rock & mineral set, make sure it's a good size, like this 100-sample monster (USD 70). Or go for the novelty value of fluorescent specimens (USD 45) — calcite, sphalerite, and the like.

If minerals seem passé for a geologist, then take the pure line with a tour of the elements. This set — the last of it's kind, by the way — costs USD 565, but it looks amazing. Yet it can't hold a candle to this beauty, all USD 5000 of it — which I badly want but let's face it will never get.

Home

If you have a rock collection, maybe you want a mineralogical tray (USD 35) to put them in? The same store has all sorts of printed fabrics by designers Elena Kulikova and Karina Eibitova. Or how about some bedding?

These steampunk light switch plates are brilliant and varied (USD 50). Not geological at all, just awesome.

I don't think they are for sale, but check out Ohio artist Alan Spencer's ceramic pieces reflecting each of the major geological periods. They're pretty amazing.

Lego

My kids are really into Lego at the moment. Turns out there are all sorts of sciencey kits you can get. I think the Arctic Base Camp (USD 90) is my favourite that's available at the moment, and it contains some kind of geological-looking type (right).

I don't condone the watching of television programmes, except Doctor Who obviously, but they do sometimes make fun Lego sets. So there's the Doctor, naturally, and other things like Big Bang Theory.

You can fiddle with these while you wait for the awesome HMS Beagle model to come out.

Books etc.

A proven success — winner of the Royal Society's prestigious Winton Prize for science books this year — is Adventures in the Anthropocene: A Journey to the Heart of the Planet We Made, by Gaia Vince, Milkweed Editions, September 2015. Available in hardback and paperback.

Lisa Randall's Dark Matter and the Dinosaurs: The Astounding Interconnectedness of the Universe (HarperCollins) just came out, and is doing remarkably well at the moment. It's getting decent reviews too. Randall is a cosmologist, and she reckons the dinosaurs were obliterated by a comet nudged out of orbit by mysteriousness. Hardback only.

If those don't do it for you, I reviewed some sciencey comic books recently... or there's always Randall Munroe.

Or you could try poking around in the giftological posts from 2011, 2012, 2013, or 2014.

Still nothing? OK, well, there's always chocolate :)

The images in this post are all someone else's copyright and are used here under fair use guidelines. I'm hoping the owners are cool with people helping them sell stuff!

The hack is back: learn new skills in New Orleans

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Looking for a way to broaden your skills for the next phase of your career? Need some networking that isn't just exchanging business cards? Maybe you just need a reminder that subsurface geoscience is the funnest thing ever? I have something for you...

It's the third Geophysics Hackathon! The most creative geoscience event of the year. Completely free, as always, and fun for everyone — not just programmers. So mark your calendar for the weekend of 17 and 18 October, sign up on your own or with a team, and come to New Orleans for the most creative 48 hours of your career so far.

What is a hackathon?

It's a fun, 2-day event full of geophysics and tech. Most people participate in teams of up to 4 people, but you can take part on your own too. There's plenty of time on the first morning to find projects to work on, or maybe you already have something in mind. At the end of the second day, we show each other what we've been working on with a short demo. There are some fun prizes for especially interesting projects.

You don't have to be a programmer to join the fun. If you're more into geological interpretation, or reservoir engineering, or graphic design, or coming up with amazing ideas — there's a place for you at the hackathon. 

FAQ

  • How much does it cost? It's completely free!
  • I don't believe you. Believe it. Coffee and tacos will be provided. Just bring a laptop.
  • When is it? 17 and 18 October, doors open at 8 am each day, and we go till about 5.30.
  • So I won't miss the SEG Icebreaker? No, we'll all go!
  • Where is it? Propeller, 4035 Washington Avenue, New Orleans
  • How do I sign up? Find out more and register for the event at ageo.co/geohack15

Being part of it all

If this all sounds awesome to you, and you'll be in New Orleans this October, sign up! If you don't think it's for you, please drop in for a visit and a coffee — give me a chance to convince you to sign up next time.

If you own or work for an organization that wants to see more innovation in the world, please think about sponsoring this event, or a future one.

Last thing: I'd really appreciate any signal boost you can offer — please consider forwarding this post to the most creative geoscientist you know, especially if they're in the Houston and New Orleans area. I'm hoping that, with your help, this can be our biggest event ever.

Seismic inception

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A month ago, some engineers at Google blogged about how they had turned a deep learning network in on itself and produced some fascinating and/or disturbing images:

One of the images produced by the team at Google. Click to see a larger version. Read more. CC-BY.

The basic recipe, which Google later open sourced, involves training a deep learning network (basically a multi-layer neural network) on some labeled images, animals maybe, then searching for matching patterns in a target image, like these clouds. If it finds something, it emphasizes it — given the data, it tries to construct an animal. Then do it again.

Or, here's how a Google programmer puts it (one of my favourite sentences ever)...

Making the "dream" images is very simple. Essentially it is just a gradient ascent process that tries to maximize the L2 norm of activations of a particular DNN layer. 

That's all! Anyway, the point is that you get utter weirdness:

OK, cool... what happens if you feed it seismic?

That was my first thought, I'm sure it was yours too. The second thing I thought, and the third, and the fourth, was: wow, this software is hard to compile. I spent an unreasonable amount of time getting caffe, the Berkeley Vision & Learning Centre's deep learning software, working. But on Friday I cracked it, so today I got to satisfy my curiosity.

The short answer is: reptiles. These weirdos were 8 levels down, which takes about 20 minutes to reach on my iMac.

Seismic data from the Virtual Seismic Atlas, courtesy of Fugro. 

THE DEEPDREAM TREATMENT. Mostly reptiles.

Er, right... what's the point in all this?

That's a good question. It's just a bit of fun really. But it makes you wonder:

  • What if we train the network on seismic facies? I think this could be very interesting.
  • Better yet, what if we train it on geology? Probably spurious: seismic is not geology.
  • Does this mean learning networks are just dumb machines, or can they see more than us? Tough one — human vision is highly fallible. There are endless illusions to prove this. But computers only do what we tell them, at least for now. I think if we're careful what we ask for, we can use these highly non-linear data-crunching algorithms for good.
  • Are we out of a job? Definitely not. How do you think machines will know what to learn? The challenge here is to make this work, and then figure out how it can help change, or at least accelerate, our understanding of the subsurface.

This deep learning stuff — of which the University of Toronto was a major pioneer during its emergence in about 2010 — is part of the machine learning revolution that you are, like it or not, experiencing. It will take time, and it will make awful mistakes, but the indications are that machine learning will eat every analytical method for breakfast. Customer behaviour prediction, computer vision, natural language processing, all this stuff is reeling from the relatively sudden and widespread availability of inexpensive computer intelligence. 

So what are we going to do with that?

           Okay, one more. from Paige Bailey's Twitter feed.

           Okay, one more. from Paige Bailey's Twitter feed.

Pick This again

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Since I last wrote about it, Pick This! has matured. We have continued to improve the tool, which is a collaboration between Agile and the 100% awesome Steve Purves at Euclidity.

Here's some of the new stuff we've added:

  • Multiple lines and polygons for each interpretation. This was a big limitation; now we can pick multiple fault sticks, say.
  • 'Preshows', to show the interpreter some text or an image before they interpret. In beta, talk to us if you want to try it.
  • Interpreter cohorts, with randomized selection, so we can conduct blind trials.  In beta, again, talk to us.
  • Complete picking history, so we can replay the entire act of interpretation. Coming soon: new visualizations of results that use this data.

Some of this, such as replaying the entire picking event, is of interest to researchers who want to know how experts interpret images. Remotely sensed images — whether in geophysics, radiology, astronomy, or forensics — are almost always ambiguous. Look at these faults, for example. How many are there? Where are they exactly? Where are their tips?  

A seismic line from the Browse Basin, offshore western Australia. Data courtesy of CGG and the Virtual Seismic Atlas

A seismic line from the Browse Basin, offshore western Australia. Data courtesy of CGG and the Virtual Seismic Atlas

Most of the challenges on the site are just fun challenges, but some — like the Browse Basin challenge, above — are part of an experiment by researchers Juan Alcalde and Clare Bond at the University of Aberdeen. Please help them with their research by taking part and making an interpretation! It would also be super if you could fill out your profile page — that will help Juan and Clare understand the results. 

If you're at the AAPG conference in Denver then you can win bonus points by stopping by Booth 404 to visit Juan and Clare. Ask them all about their fascinating research, and say hello from us!

While you're on the site, check out some of the other images — or upload one yourself! This one was a real eye-opener: time-lapse seismic reflections from the water column, revealing dynamic thermohaline stratification. Can you pick this?

Pick This challenge showing time-lapse frames from a marine 3D. The seabed is shown in blue at the bottom of the images.

Pick This challenge showing time-lapse frames from a marine 3D. The seabed is shown in blue at the bottom of the images.

Minecraft for geoscience

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The Isle of Wight, complete with geology. ©Crown copyright. 

The Isle of Wight, complete with geology. ©Crown copyright. 

You might have heard of Minecraft. If you live with any children, then you definitely have. It's a computer game, but it's a little unusual — there isn't really a score, and the gameplay has no particular goal or narrative, leaving everything to the player or players. It's more like playing with Lego than, say, playing chess or tennis or paintball. The game was created by Swede Markus Persson and then marketed by his company Mojang. Microsoft bought Mojang in September last year for $2.5 billion. 

What does this have to do with geoscience?

Apart from being played by 100 million people, the game has attracted a lot of attention from geospatial nerds over the last 12–18 months. Or rather, the Minecraft environment has. The game chiefly consists of fabricating, placing and breaking 1-m-cubed blocks of various materials. Even in normal use, people create remarkable structures, and I don't just mean 'big' or 'cool', I mean truly remarkable. So the attention from the British Geological Survey and the Danish Geodata Agency. If you've spent any time building geocellular models, then the process of constructing elaborate digital models is familiar to you. And perhaps it's not too big a leap to see how the virtual world of Minecraft could be an interesting way to model the subsurface. 

Still I was surprised when, chatting to Thomas Rapstine at the Geophysics Hackathon in Denver, he mentioned Joe Capriotti and Yaoguo Li, fellow researchers at Colorado School of Mines. Faced with the problem of building 3D earth models for simulating geophysical experiments — a problem we've faced with modelr.io — they hit on the idea of adapting Minecraft models. This is not just a gimmick, because Minecraft is specifically designed for simulating and manipulating landscapes.

The Minecraft model (left) and synthetic gravity data (right). Image ©2014 SEG and Capriotti & Li. Used in acordance with SEG's permissions. 

The Minecraft model (left) and synthetic gravity data (right). Image ©2014 SEG and Capriotti & Li. Used in acordance with SEG's permissions. 

If you'd like to dabble in geospatial Minecraft yourself, the FME software from Safe now has a standardized way to get Minecraft data into and out of the environment. Essentially they treat the blocks as point clouds (e.g. as you might get from Lidar or a laser scan), so they can do conventional operations, such as differences or filtering, with the software. They recorded a webinar on the subject yesterday.

Minecraft is here to stay

There are two other important angles to Minecraft, both good reasons why it will probably be around for a while, and probably both something to do with why Microsoft bought Mojang...

  1. It is a programming gateway drug. Like web coding, and image processing, Minecraft might be another way to get people, especially young people, interested in computing. The tiny Linux machine Raspberry Pi comes with a version of the game with a full Python API, so you can control the game programmatically.  
  2. Its potential beyond programming as a STEM teaching aid and engagement tool. Here's another example. Indeed, the United Nations is involved in Block By Block, an effort around collaborative public space design echoing the Blockholm project, an early attempt to explore social city planning in the tool.

All of which is enough to make me more curious about the crazy-sounding world my kids have built, with its Houston-like city planning: house, school, house, Home Sense, house, rocket launch pad...

References

Capriotti, J and Yaoguo Li (2014) Gravity and gravity gradient data: Understanding their information content through joint inversions. SEG Technical Program Expanded Abstracts 2014: pp. 1329-1333. DOI 10.1190/segam2014-1581.1 

The thumbnail image is from an image by Terry Madeley.

UPDATE: Thank you to Andy for pointing out that Yaoguo Li is a prof, not a student.

2014 retrospective

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At this time of year, we look back at the best of the blog — what were the most read, the most contentious, the most informative posts of the year? If you only stop by once every 12 months, this is the post for you!

Your favourites

Let's turn to the data first. Which posts got the most hits this year? Older posts have a time advantage of course, but here are the most popular new posts, starting with the SEG-Y double-bill:

It's hard to say exactly how much attention a given post gets, because they sit on the front page of the site for a couple of weeks. Overall we got about 150 000 pageviews this year, and I think Well tie workflow — the most-read old post on the site this year — might have been read (okay, looked at) 5000 or so times.

I do love how some of our posts keep on giving: none of the top posts this year topped this year's readership of some golden oldies: Well tie workflow (written in April 2013), Six books about seismic interpretation (March 2013), k is for wavenumber (May 2012), Interpreting spectral gamma-ray logs (February 2013), or Polarity cartoons (April 2012).

What got people talking

When it all goes quiet on the comments, I worry that we're not provocative enough. But some posts provoke a good deal of chat, and always bring more clarity and depth to the issue. Don't miss the comments in Lusi's 8th birthday...

Our favourites

We have our favourites too. Perhaps because a lot of work went into them (like Evan's posts about programming), or because they felt like important things to say (as in the 'two sides' post), or because they feel like part of a bigger idea.

Where is everybody?

We don't collect detailed demographic data, but it's fun to see how people are reading, and roughly where they are. One surprise: the number of mobile readers did not rise this year — it's still about 15%. The top 10 cities were

Agile_top_60plus_cities_2014.png
  1. Houston, USA
  2. Calgary, Canada
  3. London, UK
  4. Perth, Australia
  5. Ludwigshafen, Germany
  6. Denver, USA
  7. Aberdeen, UK
  8. Moscow, Russia
  9. Stavanger, Norway
  10. Kuala Lumpur, Malaysia

Last thing

Thank You for reading! Seriously: we want to be a useful and interesting part of our community, so every glance at our posts, every comment, and every share, help us figure out how to be more useful and more interesting. We aim to get better still next year, with more tips and tricks, more code, more rants, and more conference reports — we look forward to sharing everything Agile with you in 2015.

If this week is Christmas for you, then enjoy the season. All the best for the new year!

Previous Retrospective posts... 2011 retrospective •  2012 retrospective • 2013 retrospective

The new open geophysics tools

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The hackathon in Denver was more than 6 weeks ago. I kept thinking, "Oh, I must post a review of what went down" (beyond the quick wrap-up I did at the time), but while I'm a firm believer in procrastination six weeks seems unreasonable... Maybe it's taken this long to scrub down to the lasting lessons. Before those, I want to tell you who the teams were, what they did, and where you can find their (100% open source!) stuff. Enjoy!

Geophys Wiz

Andrew Pethick, Josh Poirier, Colton Kohnke, Katerina Gonzales, and Elijah Thomas — GitHub repo

This team had no trouble coming up with ideas — perhaps a reflection of their composition, which was more heterogeneous than the other teams. Josh is at NEOS, the consulting and software firm, and Andrew is a postdoc at Curtin in Perth, Australia, while the other 3 are students at Mines. The team eventually settled on building MT Black Box, a magnetotellurics modeling web application. 

Last thing: Don't miss Andrew Pethick's write-up of the event. 

Seemingly Concerned Neighbours

Elias Arias, Brent Putman, Thomas Rapstine, and Gabriel Martinez — Github repo

These four young geophysicists from the Colorado School of Mines impressed everyone with their work ethic. Their tight-knit team came in with a plan, and proceeded to scribble up the coolest-looking whiteboard of the weekend. After learning some Android development skills 'earlier this week', they pulled together a great little app for forward modeling magnetotelluric responses. 

Hackathon_well_tie_guys.jpg

Well tie guys

Michaël Montouchet, Graham Dawes, Mark Roberts

It was terrific to have pro coders Graham and Michaël with us — they flew from the UK to be with us, thanks to their employer and generous sponsor ffA GeoTeric. They hooked up with Mark, a Denver geophysicist and developer, and hacked on a well-tie web application, rightly identifying a gap in the open source market, so to speak (there is precious little out there for well-based workflows). They may have bitten off more than they could chew in just 2 days, so I hope we can get together with them again to finish it off. Who's up for a European hackathon? 

These two characters from UBC didn't get going till Sunday morning, but in just five hours they built a sweet web app for forward modeling the DC resistivity response of a buried disk. They weren't starting from scratch, because Rowan and others have spent months honing SimPEG, a rich open-source geophysical library, but minds were nonetheless blown.

Key takeaway: interactivity beyond sliders for the win.

Pick This!

Ben Bougher, Jacob Foshee, Evan Bianco, and an immiscible mixture of Chris Chalcraft and me — GitHub repo

Wouldn't you sometimes like to know how other people would interpret the section you're working on? This team, a reprise of the dream team from Houston in 2013, built a simple way to share images and invite others to interpret them. When someone has completed their interpretation, only then do they get to see the ensemble — everyone else's interpretations — in a heatmap. Not only did this team demo live software at pickthis.io, but the audience provided the first crowdsourced picks in real time. 

We'll be blogging more about Pick This soon. We're actively seeking ideas, images, interpreters, and financial support. Keep an eye out.

What I learned at this hackathon

  • Potential fields are an actual thing! OK, kidding, but three out of five teams built potential field modeling tools. I wasn't expecting that, and I think the judges were impressed at the breadth. 
  • 30 hours is easily enough time to build something pretty cool. Heck, 5 hours is enough if you're made of the right stuff. 
  • Students can happily build prototypes alongside professional developers, and even teach them a thing or two. And vice versa. Are hackathons a leveller of playing fields?
  • We need to remove the road blocks to more people enjoying this event. To help with this, next time there will be a 1-day bootcamp before the hackathon.
  • After virtually doubling in size from 2013 to 2014, it's clear that the 2015 Hackathon in New Orleans is going to be awesome! Mark your calendar: 17 and 18 October 2015.

Thank you!

Thank you to the creative, energetic geophysicists that came. It was a privilege to meet and hack with you!

Thank you to the judges who gave up their Sunday teatime to watch the demos and give precious feedback to the teams: Steve Adcock, Jamie Allison, Maitri Erwin, Dennis Cooke, Chris Krohn, Shannon Bjarnason, David Holmes, and Tracy Stark. Amazing people, one and all.

A final Thank You to our sponsors — dGB Earth Sciences, ffA GeoTeric, and OpenGeoSolutions. You guys are totally awesome! Seriously.

sponsors_white_noagile.png

It's the GGGG (giant geoscience gift guide)

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I expect you've been wondering what to get me and Evan for Christmas. Wonder no more! Or, if you aren't that into Agile, I suppose other geoscientists might even like some of this stuff. If you're feeling more needy than generous, just leave this post up on a computer where people who love you will definitely see it, or print it out and mail it to everyone you know with prominent red arrows pointing to the things you like best. That's what I do.

Geology in the home

Paul_Smith_rug.jpg

Art!

Museums and trips and stuff

Image is CC-BY by Greg Westfall on Flickr

Image is CC-BY by Greg Westfall on Flickr

Geo-apparel

Blimey... books!

Who over the age of 21 or maybe 30 doesn't love getting books for Christmas? I don't!... not love it. Er, anyway, here are some great reads!

  • How about 156 things for the price of three? Yeah, that is a deal.
  • They're not geological but my two favourite books of the year were highly geeky — What If? by Randall Munroe and Cool Tools by Kevin Kelly.
  • Let's face it, you're going to get books for the kids in your life too (I hope). You can't do better than Jon Tennant's Excavate! Dinosaurs.
  • You're gonna need some bookends for all these books.

Still stuck? Come on!

All of the smaller images in this post are copyright of their respective owners, and I'm hoping they don't mind me using them to help sell their stuff.

Update on 2014-12-12 01:41 by Matt Hall
​In case you're still struggling, Evelyn Mervine has posted her annual list over on the AGU Blogosphere. If you find any more geo-inspired gift lists, or have ideas for others, please drop them in the comments.