Maitri

Regular readers will remember the Unsolved Problems Unsession at the GeoConvention in Calgary last May. We think these experiments in collaboration are one possible way to get people more involved in progressing geoscience at conferences, and having something to show for it. We plan to do more — and are here to support you if you'd like to try one in your community.

Last Thursday was the 2014 CSEG Symposium. The organizers asked me for a short video to sum up what happened at the unsession for the crowd, and to help get them in the mood for some discussion. I hope it helped...

Getting better

Conferences seem so crammed with talks these days. No time for good conversation, in or out of the sessions. The only decent discussion I remember recently (apart from the unsession, obvsly) was at EAGE in 2012, when a talk finished early and the space filled with a fascinating discussion between two compressed sensing clever-clogs.

I think there are a few ways to get better at it:

• Make more time for it, preferably at least 40 minutes.
• Get people into smaller groups, about 4–12 people is good.
• Facilitate with some ground rules, provocative questions, and conversation management.
• Capture what was said, preferably in real time and using the participants' own words.
• Use lots of methods: drawing, sticky notes, tweets, video, and so on.
• Reflect the conversation back at the participants, and let them respond.
• Read up on open space, knowledge café, charrettes, and other methods.
• Don't shut it down with "I guess we're out of time..." — review or sum up first.

Think about when you have been part of a really good conversation. How it feels, how it flows, and how you remember it for days afterwards, and mention it to others later. I think we can have more of those about our work, and conferences are a great place to help them happen.

Stay tuned for details of the next unsession — again, at the Calgary GeoConvention.

This was originally posted at: http://blogs.egu.eu/palaeoblog/?p=1138

For some time now, there has been much debate about whether our beloved dinosaur, Triceratops, is a distinct species, or a younger version of a bigger ceratopsian, Torosaurus – the great Toroceratops’ debate. Proponents of both sides of the argument have made detailed quantitative and qualitative points, and there doesn’t really seem to have been any resolution. Check out the video below for a great discussion of the issues, or this link or this link.

Enter geometric morphometrics (GM). Everyones’ favourite-sounding method, GM is essentially a way of analysing the shape of objects, like fossils, using co-ordinate data. There are a range of statistical ways of spanking your data into shape once you have a digital version of it, and have converted an object into a series of point co-ordinates (decent-ish explanation in the methods section here).

What it is for scientists is a way of introducing statistical rigour to test a hypothesis. It’s really frickin’ useful, pretty much. The hypothesis which Maironi et al. wanted to test was whether Triceratops, Torosaurus, and Nedoceratops, another dino that might be just a younger Torosaurus, were distinct enough to not be regarded as a single growth series of the same species. Using geometric morphometrics, it is possible to visit the shape variation that specimens exhibit, as well as whether they truly represent discrete groups.

I didn’t want to this post to be critical of the methods for this paper, but they have missed a few essential steps. If you want to test for discrete clusters or groups within your data, principal components analysis (PCA) is not really the right method, as this study uses. PCA is a way of taking a high-dimensional data set, as you usually get using GM, and reducing it into fewer variables that represent a high proportion of the variance within that data set – usually, 95% of the variance is the accepted minimum required to be represented by a number of principal components.

In this case, 12 (!) PCs represented 95% of the variance in the reconstructed digital dinos. The first two only represent about 60% of the data – it is, then, entirely inappropriate to analyse just these two when they represent such a small proportion of the original data. What the study essentially does, is attempts to interpret distinctiveness of the different species, in a ‘morphospace’ that firstly isn’t designed to test for distinctiveness, but also fails to faithfully represent the data. Ideally, you’d want to analyse the dispersion pattern of all of the specimens with respect to the first 12 axes – this would tell you about the shape changes that are being represented by each axis.

The next step should have been to use a form off discriminant analysis – these tests are designed to test for group distinctiveness, as they incorporate group-level information as an additional variable; in this case, the species’ ID. Performing this would tell you how accurate, or distinct, your supposedly different groups are, and you can test the proportion of specimens that are correctly ‘assigned’ to each group. I go into this protocol in some detail in a forthcoming paper, and will discuss it more then. For now, I feel a bit bad saying, but this is really only half an analysis, and a lot more could have been and should have been done with it.

Nonetheless, there are some interesting results, if not based on an entirely substantial analysis (imo). Importantly, Torosaurus and Triceratops, in the context of the first two principal components, occupy different morphospaces, which suggests that they can be delimited based on shape as well as their sizes. That’s pretty much it. Another piece of the puzzle suggesting that we can keep Triceratops alive, for now!

Fortunately, the authors have been jolly decent uploaded their raw data, so I’m gonna go have a play with it and see what we get.. BRB

Reference:

Maiorini, L., Farke, A. A., Kotsakis, T. and Piras, P. (2013) Is Torosaurus Triceratops? Geometric morphometric evidence of Late Maastrichtian ceratopsid dinosaurs, PLOS ONE, 8(11), e81608 (OA link)

Filed under: Fossils, Homology, Palaeontology Tagged: Geometric Morphometrics, Toroceratops, Torosaurus, Triceratops

GEOPHYSICS, Volume 79, Issue 2, Page D115-D121, March-April 2014.

A 4.4 magnitude earthquake hit the Los Angeles area this morning. Yesterday, northern Chile was rocked by a 6.7 bone shaker. This seems like a nice time to link to Michelle Lanz' piece from earlier this year chronicling some common earthquake myths. One big one: Doorways aren't actually sanctuary. That idea has its origins in a time and place where most houses were made out of adobe. Today, you're better off dropping to the floor and crawling underneath something sturdy.

Last week Teju Cole published a 4,000-word non-fiction essay on immigration, titled “A Piece of the Wall,” entirely on Twitter. BuzzFeed spoke with Cole about his decision to share the piece via the social media platform, the challenges in doing so, and his views on immigration reform:

I’m not getting my hopes up, but the point of writing about these things, and hoping they reach a big audience, has nothing to do with “innovation” or with “writing.” It’s about the hope that more and more people will have their conscience moved about the plight of other human beings. In the case of drones, for example, I think that all the writing and sorrow about it has led to a scaling back of operations: It continues, it’s still awful, but the rate has been scaled back, and this has been in specific response to public criticism. I continue to believe the emperor has a soul.

Related Posts:

• Second Twitter Fiction Festival Approaches
• The Faces of Immigration 100 Years Ago
• What Artist is the Focus of Your Unconditional Affection?
• Trending Now: The Internet Knows Your Secrets
• The Rumpus Interview with Adriana Páramo

It seems that at least once a year the voices of an outraged few raise the topic of women’s underrepresentation in leadership positions. But just as quickly, the subject retreats underground for a prolonged period of chilly status quo, like Punxsutawney Phil after spying a shadow. This happened again last month when Catalyst reported another year of essentially no growth for women in corporate leadership positions. According to the nonprofit focused on women and business, women held 16.9 percent…

Industrial Soundtrack for the Urban Decay is a forthcoming documentary about industrial music featuring BB pals Throbbing Gristle and V Vale (RE/Search) along with Cabaret Voltaire, NON, Z'EV, Sordide Sentimental, SPK, and many more artists/thinkers. Directed by Amélie Ravalec and Travis Collins, the film is in post-production and slated for release later this year.

What are your favorite geosites — cool geologic formations, awe-inspiring landscapes of rock, related museum exhibits, or even buildings made from particularly fascinating stones?

The Geological Society of London is asking people to submit their favorite geosites in the UK and Ireland. You can get in on that challenge via Twitter, Facebook, or emailing the Society at 100geosites@geolsoc.org.uk. But that got me thinking about geosites elsewhere. What would you nominate for a list of the best geosites in the world?

One of my favorites is definitely the Flint Hills, rolling limestone hills in central Kansas that are cut through with narrow, deep creek ravines and covered with tallgrass prairie.

You can see neat cutaways of the Flint Hills geology, where highway workers blasted through some of the hills to clear the path of I-70 between Topeka and Salina. Despite the lush look the prairie gives the hills, in reality there's not much dirt for growing anything here. Just layer upon layer of rock with a fuzz of grass on top, like a giant chia pet.

The Flint Hills are the remains of one of the times that Kansas was part of a shallow, inland sea — in this case, during the Permian, about 286 to 245 million years ago. All that limestone is made from the skeletons, shells, and other calcium-rich structures of oysters, coral, sea urchins, and more.

Image: Jim Minnerath / USFWS

Enjoy the greatest tradition of the holiday: science-themed limericks!

Controlling the spread of sound and how it bounces off objects is not easy. But by using a few perforated sheets of plastic and a complex algorithm, researchers at Duke University have developed the world's first 3D acoustic cloaking device.

Read more...

For a show as all-encompassing as Cosmos, it’s surprising that the series’ only reference to evolution so far lasted less than a minute. And if you live in Oklahoma City, Fox News affiliate KOKH-TV didn’t even want you to see that.

Youtube user Adam Bates recorded the news outlet’s painfully obvious attempt to edit out Neil deGrasse Tyson’s poetic words:

Before watching the clip I was willing believe KOKH-TV’s conveniently placed ad was an act of stupidity and not censorship, but the unbelievably bizarre editing makes it pretty clear that this commercial break was just a poorly disguised attempt to cut some science out of a science show. Honestly, I’m surprised the news clip doesn’t claim that “their biggest earthquake” was punishment for the Spaceship of the Imagination.

If  you were one of the Oklahoma viewers whose broadcast was rudely  interrupted, here’s Cosmos‘ entire text thus far on evolution:

We are newcomers to the Cosmos…Our own story only begins on the last night of the cosmic year…Three and a half million years ago, our ancestors — your and mine left these traces. We stood up and parted ways from them. Once we were standing on two feet, our eyes were no longer fixated on the ground. Now, we were free to look up and wonder.

As far as a statement of beliefs on evolution goes, Cosmos‘ script could have been far more divisive. If those relatively mild 30 seconds offended KOKH-TV, they should hire better editors and strap in for a wild ride. As one Youtube commenter points out, “just wait until they start addressing man-made climate change”.

(via Uproxx, images via Cosmos)

Meanwhile in related links

• Wonder how FOX feels about Obama’s connection?
• The ratings are in!
• Missouri bill would alert parents when evolution will be taught

Ever since reporters began publishing stories about NSA activities, based on documents provided by Edward Snowden, we've been repeatedly assured by government officials that it's "only metadata." This might fool the average person, but it shouldn't fool those of us in the security field. Metadata equals surveillance data, and collecting metadata on people means putting them under surveillance.

An easy thought experiment demonstrates this. Imagine that you hired a private detective to eavesdrop on a subject. That detective would plant a bug in that subject's home, office, and car. He would eavesdrop on his computer. He would listen in on that subject's conversations, both face to face and remotely, and you would get a report on what was said in those conversations. (This is what President Obama repeatedly reassures us isn't happening with our phone calls. But am I the only one who finds it suspicious that he always uses very specific words? "The NSA is not listening in on your phone calls." This leaves open the possibility that the NSA is recording, transcribing, and analyzing your phone calls -- and very occasionally reading them. This is far more likely to be true, and something a pedantically minded president could claim he wasn't lying about.)

Now imagine that you asked that same private detective to put a subject under constant surveillance. You would get a different report, one that included things like where he went, what he did, who he spoke to -- and for how long -- who he wrote to, what he read, and what he purchased. This is all metadata, data we know the NSA is collecting. So when the president says that it's only metadata, what you should really hear is that we're all under constant and ubiquitous surveillance.

What's missing from much of the discussion about the NSA's activities is what they're doing with all of this surveillance data. The newspapers focus on what's being collected, not on how it's being analyzed -- with the singular exception of the Washington Post story on cell phone location collection. By their nature, cell phones are tracking devices. For a network to connect calls, it needs to know which cell the phone is located in. In an urban area, this narrows a phone's location to a few blocks. GPS data, transmitted across the network by far too many apps, locates a phone even more precisely. Collecting this data in bulk, which is what the NSA does, effectively puts everyone under physical surveillance.

This is new. Police could always tail a suspect, but now they can tail everyone - suspect or not. And once they're able to do that, they can perform analyses that weren't otherwise possible. The Washington Post reported two examples. One, you can look for pairs of phones that move toward each other, turn off for an hour or so, and then turn themselves back on while moving away from each other. In other words, you can look for secret meetings. Two, you can locate specific phones of interest and then look for other phones that move geographically in synch with those phones. In other words, you can look for someone physically tailing someone else. I'm sure there are dozens of other clever analyses you can perform with a database like this. We need more researchers thinking about the possibilities. I can assure you that the world's intelligence agencies are conducting this research.

How could a secret police use other surveillance databases: everyone's calling records, everyone's purchasing habits, everyone's browsing history, everyone's Facebook and Twitter history? How could these databases be combined in interesting ways? We need more research on the emergent properties of ubiquitous electronic surveillance.

We can't protect against what we don't understand. And whatever you think of the NSA or the other 5-Eyes countries, these techniques aren't solely theirs. They're being used by many countries to intimidate and control their populations. In a few years, they'll be used by corporations for psychological manipulation -- persuasion or advertising -- and even sooner by cybercriminals for more illicit purposes.

This essay previously appeared in the March/April 2014 issue of IEEE Security and Privacy.

EDITED TO ADD (3/14): This study of cellphone meta-data (news article here) demonstrates the point nicely. So does this amicus brief I signed in the ACLU v. Clapper case (press release here).

As “The Science Guy,” Our Friend Bill Nye helped shape a lot of young minds. (Ours included.) In this new promo for his upcoming episode of the PBS series NOVA: The Secret Lives of Scientists, he talks about how he moved from engineering to science entertainment.

We’ll have some exclusive Bill Nye videos coming your way soon that we shot with him at SXSW, but for now, you’re just going to have to settle for this one. If this isn’t enough for you, PBS will be releasing more videos with Bill over the next two weeks, and so will we!

(via NOVA: The Secret Lives of Scientists)

Meanwhile in related links

• He also talked about bow ties for the show
• Bill’s debate with creationist Ken Ham will help fund Ham’s ark
• Bill Nye got into a global warming non-debate on Meet the Press

France Cordova takes the helm of the National Science Foundation at a time of tight federal budgets for science

-- Read more on ScientificAmerican.com

We already knew that the NSA has weaponized the internet, enabling them to "shoot" exploits at anyone they desire. But the Edward Snowden slides and story published yesterday convey a wealth of new detailed information about the NSA's technology and its limitations.

Pertinent question about the blockbuster Mr. Peabody & Sherman animated feature: Why?

alphadogg writes "Having lots of Wi-Fi networks packed into a condominium or apartment building can hurt everyone's wireless performance, but Stanford University researchers say they've found a way to turn crowding into an advantage. In a dorm on the Stanford campus, they're building a single, dense Wi-Fi infrastructure that each resident can use and manage like their own private network. That means the shared system, called BeHop, can be centrally managed for maximum performance and efficiency while users still assign their own SSIDs, passwords and other settings. The Stanford project is making this happen with inexpensive, consumer-grade access points and SDN (software-defined networking)."

Read more of this story at Slashdot.

This is one of my favourite knowledge sharing stories.

A farmer in my community had a problem with one of his cows — it was seriously unwell. He asked one of the old local farmers about the symptoms, and was told, “Oh yes, one of my herd had the same thing last summer. I gave her a cup of brandy and four aspirins every night for a week.” The young farmer went off and did this, but the poor cow got steadily worse and died. When he saw the old farmer next he told him, more than a little accusingly, “I did what you said, and the cow died anyway.” The old geezer looked into the distance and just said, “Yep, so did mine.”

Incomplete information can be less useful than no information. Yet incomplete information has somehow become our specialty in applied geoscience. How often do we share methods, results, or case studies without the critical details that would make it useful information? That is, not just marketing, or resumé padding. Inded, I heard this week that one large US operator will not approve a publication that does include these critical details! And we call ourselves scientists...

Completeness mandatory

Thankfully, Last month The Leading Edge — the magazine of the SEG — started a new tutorial column, edited by me. Well, I say 'edited', I'm just the person that pesters prospective authors until they give in and send me a manuscript. Tad Smith, Don Herron, and Jenny Kucera are the people that make it actually happen. But I get to take all the credit.

When I was asked about it, I suggested two things:

1. Make each tutorial reproducible by publishing the code that makes the figures.
2. Make the words, the data, and the code completely open and shareable. 

To my delight and, I admit, slight surprise, they said 'Sure!'. So the words are published under an open license (Creative Commons Attribution-ShareAlike, the same license for re-use that most of Wikipedia has), the tutorials use open data for everything, and the code is openly available and free to re-use. Complete transparency.

There's another interesting aspect to how the column is turning out. The first two episodes tell part of the story in IPython Notebook, a truly amazing executable writing environment that we've written about before. This enables you to seamlessly stich together text, code, and plots (left). If you know a bit of Python, or want to start learning it right now this second, go give wakari.io a try. It's pretty great. (If you really like it, come and learn more with us!).

Read the first tutorial: Hall, M. (2014). Smoothing surfaces and attributes. The Leading Edge, 33(2), 128–129. doi: 10.1190/tle33020128.1. A version of it is also on SEG Wiki, and you can read the IPython Notebook at nbviewer.org.

Do you fancy authoring something for this column? Wonderful — please do! Here are the author instructions. If you have an idea for something, please drop me a line, let's talk about how to make it relentlessly practical.

Female representation in games is mired in toxic archetypes, so much so that even conscious efforts to avoid or neutralize them tends to end up mirroring the problem. The makers of Desktop Dungeons, however, are taking a more considered approach.

It wasn’t good enough for us to simply react with deliberate ugliness or typically masculine factors – the idea was for Desktop Dungeons to remove the gender binary entirely instead of just making everyone a man. In de-emphasising sex as much as possible, we hoped that players would be able to enjoy a more gender agnostic environment in general. Some of our proudest mechanical tweaks involved removing notices and choices in particular areas. ... .Shorthands for the feminine kept crawling into our work when we weren’t paying attention – smooth skin, homogenised facial structures, evidence of makeup, you name it. Even characters who we thought would easily sidestep trouble (like the female wizard) simply looked like young, pretty women in grunge costume rather than hardboiled dungeoneers. Portraits for some species went through several drafts just to deprogram our subconscious idea of what felt normal and right.

Hugh Pickens DOT Com writes "Amanda Solliday reports at Symmetry that six months ago, organizers of a biweekly forum on Large Hadron Collider physics at Fermilab banned PowerPoint presentations in favor of old-fashioned, chalkboard-style talks. 'Without slides, the participants go further off-script, with more interaction and curiosity,' says Andrew Askew. 'We wanted to draw out the importance of the audience.' In one recent meeting, physics professor John Paul Chou of Rutgers University presented to a full room holding a single page of handwritten notes and a marker. The talk became more dialogue than monologue as members of the audience, freed from their usual need to follow a series of information-stuffed slides flying by at top speed, managed to interrupt with questions and comments. Elliot Hughes, a Rutgers University doctoral student and a participant in the forum, says the ban on slides has encouraged the physicists to connect with their audience. 'Frequently, in physics, presenters design slides for people who didn't even listen to the talk in the first place,' says Hughes. 'In my experience, the best talks could not possibly be fully understood without the speaker.'"

Read more of this story at Slashdot.

Zothecula writes "3D Systems, in collaboration with Ekso Bionics, has created a 3D-printed robotic exoskeleton that has restored the ability to walk in a woman paralyzed from the waist down. The Ekso-Suit was trialled and demonstrated by Amanda Boxtel, who was told by her doctor that she'd never walk again after a skiing accident in 1992. 'Designers from 3D Systems scanned her body, digitizing the contours of her spine, thighs, and shins, a process that helped them mold the robotic suit to her. Then they combined the suit with a set of mechanical actuators and controls made by EksoBionics. ... One problem that the designers faced in this case was that a paralyzed person like Boxtel often can't know that bruising is happening because she can't feel it. That's dangerous, Summit said, because undetected bruises or abrasions can become infected. "So we had to be very careful with creating geometry that would dodge the parts of the body that it had to dodge...[designing] parts that wouldn't impede circulation or cause bruising."'"

Read more of this story at Slashdot.

One topic that was emphasized over and over again at the MIT Enterprise Forum Texas chapter’s Feb. 19 discussion on big data was that continuing advances in data science are going to impact every single industry. Although some may consider “big data” a fad, it is actually a technology discipline that is leading to self-driving cars, programs that can grade student essays and even programs that can determine the best places to drill for oil and gas, explained Anthony Goldbloom, founder and…

Sonic booms made as the Higgs boson boiled into being could point to new physics if gravitational wave detectors can find the ripples they left behind

Source: New Scientist - Discipline: Physics

Dante's got nothing on the endless loops of interruptions, overwhelming emails and pointless formalities that plague workplaces. Here's how to break free.

Mind-numbing meetings, overflowing inboxes and urgent projects that require you to drop everything--do ever feel like parts of your workday are a personalized form of hell? If you're frustrated by ineffective work processes--and complaining to coworkers over drinks--you're not alone.

Read Full Story

Here is a short piece from yesterday's Morning Edition with a conversation between Steve Inskeep, Gene Demby, Jamelle Bouie, and myself. Embedded below is a much longer conversation covering Stand Your Ground, the logic of twice as good, and a little misquoting of King Lear. I wish Jamelle's ruminations on the work of Tony Judt had made it in. But this is still very good. It was also very therapeutic. This blog has been dressed in all black for some months now. I'm starting to get used to it.

The day before the Atlantic Geoscience Colloquium, I hosted a one-day workshop on geoscience computing to 26 maritime geoscientists. This was my third time running this course. Each time it has needed tailoring and new exercises to suit the crowd; a room full of signal-processing seismologists has a different set of familiarities than one packed with hydrologists, petrologists, and cartographers. 

Easier to consume than create

At the start of the day, I asked people to write down the top five things they spend time doing with computers. I wanted a record of the tools people use, but also to take collective stock of our creative, as opposed to consumptive, work patterns. Here's the result (right).

My assertion was that even technical people spend most of their time in relatively passive acts of consumption — browsing, emailing, and so on. Creative acts like writing, drawing, or using software were in the minority, and only a small sliver of time is spent programming. Instead of filing into a darkened room and listening to PowerPoint slides, or copying lectures notes from a chalkboard, this course was going to be different. Participation mandatory.

My goal is not to turn every geoscientist into a software developer, but to better our capacity to communicate with computers. Giving people resources and training to master this medium that warrants a new kind of creative expression. Through coaching, tutorials, and exercises, we can support and encourage each other in more powerful ways of thinking. Moreover, we can accelerate learning, and demystify computer programming by deliberately designing exercises that are familiar and relevant to geoscientists. 

Scientific computing

In the first few hours students learned about syntax, built-in functions, how and why to define and call functions, as well as how to tap into external code libraries and documentation. Scientific computing is not necessarily about algorithm theory, passing unit tests, or designing better user experiences. Scientists are above all interested in data, and data processes, helped along by rich graphical displays for story telling.

Elevation model (left), and slope magnitude (right), Cape Breton, Nova Scotia. Click to enlarge.

In the final exercise of the afternoon, students produced a topography map of Nova Scotia (above left) from a georeferenced tiff. Sure, it's the kind of thing that can be done with a GIS, and that is precisely the point. We also computed some statistical properties to answer questions like, "what is the average elevation of the province?", or "what is the steepest part of the province?". Students learned about doing calculus on surfaces as well as plotting their results. 

Programming is a learnable skill through deliberate practice. What's more, if there is one thing you can teach yourself on the internet, it is computer programming. Perhaps what is scarce though, is finding the time to commit to a training regimen. It's rare that any busy student or working professional can set aside a chunk of 8 hours to engage in some deliberate coaching and practice. A huge bonus is to do it alongside a cohort of like-minded individuals willing and motivated to endure the same graft. This is why we're so excited to offer this experience — the time, help, and support to get on with it.

How can I take the course?

We've scheduled two more episodes for the spring, conveniently aligned with the 2014 AAPG convention in Houston, and the 2014 CSPG / CSEG convention in Calgary. It would be great to see you there!

Or maybe a customized in-house course would suit your needs better? We'd love to help. Get in touch.