iGeology - BGS iPhone App

The British Geological Survey (BGS) has published a nice new application for iPhone: a geolgical map of Britain called iGeology. It is for free and with the GPS on board the phone you can find out what rock is below your feet.

• Enter a place name or postcode, or locate yourself with your phone's in-built GPS.
• Pinch open to zoom in.
• Tap on the geological map
• What are you standing on? Deposits from an ice age?
• What is the bedrock beneath the superficial deposits?
• Need a more detailed description? Follow the links to the BGS rock name database (Lexicon) and learn about the different rock formations where you are.

The geological data are served though the BGS Web Map Service (WMS)

Identification of Tsunami Deposits in the Geologic Record

Sediments deposited by tsunamis have been studied in the past as records of catastrophic events. The earthquake and tsunami that struck the Indian Ocean region on Boxing Day 2004 and claimed around 200,000 lives highlighted the need to study the sedimentary record of past tsunamis to help with planning disaster mitigation measures in coastal areas threatened by tsunamis. To help with the description and assessment of paleo-tsunami records the USGS has published an Open-File Report

Peters, Robert, and Jaffe, Bruce E. (2010): Identification of tsunami deposits in the geologic record; developing criteria using recent tsunami deposits. U.S. Geological Survey Open-File Report 2010-1239, 39 p. http://pubs.usgs.gov/of/2010/1239/.

This reminds me that I have not heard for a while about the "Mother of all Tsunamis" triggered by the Chicxulub impact. The field seems to have quieted down after 2008.

The Top of the Blogs: Geoblogosphere's weekly reviews

Geobulletin now has a new 'weekly review' page, a summary of the Geoblogosphere's weekly blogging activity.
The 'weekly review' page shows the top 10 most active and most visited blogs. It gives a rough overview on the topics treated in geoblogs by listing the most frequently used keywords and the places and stratigraphic ages most often used in blog posts. Further, it shows a list of the Geoblogosphere's top 10 blog posts based on the visits tracked at geobulletin.org.

Chinese Google Maps alternative provides geological data

Just found at Asia News:

China has launched its official online mapping service, Map World, as Google Inc has yet to apply for a Web mapping license in the country.
The State Bureau of Surveying and Mapping (SBSM) officially unveiled the free online map service on Thursday (October 21). The service will provide "comprehensive geological data", said Xu Deming, director of the SBSM, at the launch ceremony.

The tool which can be found here unfortunately is in Chinese.. so I was not able to find this feature.. Maybe one of you have been more successful?

Online lithology logs

After my first experiments with PSICAT's XML format and SVG, I have started to code a nice little tool which should allow to create lithology logs online!

The whole thing is again based on PSICAT's format. Of course it still lacks many features, however a nice new one is that the tool allows to create both, top-bottom (well logs) as well as bottom-top (outcrop logs) profiles. Astonishingly, this is not suported by most of the tools I wave seen so far.

The current version is very, very basic, it allows to create intervals, beds, to define different lithologies, grain sizes etc.. It still has no name, produces a lot of debug code, results cannot be saved (unless you copy and save the XML and the SVG), it comes without warranty and is therefore very, very alpha..

You can play with it here:
http://www.stratigraphy.net/outcrop/index.php

Don't expect too much ;)

Higher pagerank for scientific domains? Pagerank update on agenames.org

UPDATE: agenames.org's pagerank is now 0 again! very strange..

Pagerank still is the main indicator for a web site's importance. Therefore every webmaster is desperately waiting for Google's periodical pagerank update. The last update was in April 2010 and many rumours about smaller updates are circulating on the web.

Yesterday I was very surprised after I checked the rank of my brand new agenames.org domain. This domain is online since August 2010 and now has an unbelievable pagerank of 5!
I have no idea why, the site has almost no inlinks and is very young. The only reason I could imagine is that Google rewards scientific content with higher pageranks?

Visiting the Istituto Nazionale dei Geofisica e Vulcanologia

Last week I had the opportunity to visit the colleagues at the Istituto Nazionale dei Geofisica e Vulcanologia (INGV) in Rome, Italy. I was really curious about the institute. Before, I mostly was cooperating with the staff there in geoinformatics projects for sea floor observatories, but knew little about their role for the Italian earthquake warning system.

Two of my hosts, Stefano Vinci and Fawzi Doumaz proudly showed me the brand new INGV earthquake warning operation center (n.b: this is how I call it I cannot remember the real name..) and I really was very impressed: Huge flat screens everywhere showing real time seismic data from many stations. A large map of Italy gives an overview on the current seismic activity (which apparently just reloaded when I made the picture). Several operators, geoscientists of course, work there and double check the incoming seismic signals. In the background you can see the computing center where the raw data arrives and is processed. Dozens of noisy high end servers work there. Somehow, a futuristic atmosphere..

The hole system is designed around a very nice piece of software called Sismap (coded by Stefano and Fawzi) which is based on a ESRI GIS system. One of the good things about this tool is that it is integrating seismic as well as administrative data. Therefore, after a confirmed earthquake, the local authorities can immediately be informed and the system automatically generates reports for e.g. fire fighters and police. This has drastically reduced warning times and will certainly save many lives.

Some of the data is also available for the public e.g.: http://openmap.rm.ingv.it/gmaps/rec-big/Index.htm

Well and as you can see, if all breaks.. a paper copy always makes sense.

If you build it, will they come? Web 2.0 in research communication

Quite clearly, the advent of web 2.0 does not pass without effects on how researchers communicate. But how do web 2.0 technologies impact scientific communication? To find out the British Research Information Network commissioned a study and published the results in a report.

In deciding if they will make web 2.0 tools and services part of their everyday practice, the key questions for researchers are the benefits they may secure from doing so, and how it fits with their use of established services. Researchers who use web 2.0 tools and services do not see them as comparable to or substitutes for other channels and means of communication, but as having their own distinctive role for specific purposes and at particular stages of research. And frequent use of one kind of tool does not imply frequent use of others as well.

(…)

There has been considerable interest in the last two-three years in concepts of open science or open research; and in finding ways to put into effect the proposition that all kinds of information and other resources produced by researchers should flow as public goods into an open infrastructure that supports and facilitates reconfiguration and integration of those resources. Our findings show that very few researchers are as yet operating in this way. About half of respondents to our survey share their work with colleagues, but only a small group of enthusiastic open researchers – 5% of our respondents – publish their outputs and their work in progress openly, using blogs and other tools. Others consider such practices a waste of time, or even that it risks bringing ‘anarchy in science’.

The authors of this study recommend to watch the developments in this field. They do not expect immediate or short term effects on scientific communication. None of the new web 2.0 media do yet replace the traditional scientific communication media. Current users rather see the new media as a broadening of the spectrum of media available.

Procter, R., R. Williams, und J. Stewart (2010), If you build it, will they come? How researchers perceive and use web 2.0, Research Information Network, London, United Kingdom. http://www.rin.ac.uk/system/files/attachments/web_2.0_screen.pdf

Geobulletin - News from the Geoblogosphere

The last days I have worked on the new version of Geoblogosphere News which has several new and nice functions:

• First, I always found it a bit painful to type the long geoblog-stratzigraphy.net URL, so I decided to give the tool an own domain. Because every nice domain name containing geoblog etc. seems to be already sold, I bought geobulletin.org which is now the new home for Geoblogosphere News. Therefore Geoblogosphere News is now:
  
  Geobulletin: News from the Geoblogosphere

• The pages are now completely redesigned and I hope you like the new design..
• As the new LOGIN link indicates there are some new community functions. Those of you who have an OpenID (e.g. blogger or wordpress URL) can login without registration and can start playing with geobulletin.
• OpenID URLs are also used to verify a blog's owner and I plan to give you more possibilities to change the metadata of your blog.
• After login you can choose 'favorite' blog posts by clicking on a little heart icon shown after each post. These favorites are used to generate a RSS feed which you can in turn use to include it in your blogging environment.
• There is a -still experimental- DOSSIER section which can be used to give excellent posts on some 'hot topics' an own section.
  I have created 6 main categories, but this structure can be changed of course..
• I will not show google ads any more. The 2 $ monthly didn't even cover Geoblogosphere News' hosting costs ;)
  
• Well and there has been many, many code cleanups and changes etc, I therefore assume geobulletin will be a bit buggy. This is why I have added the small red 'alpha' to the headline.

Team Digital Preservation and the Planets Testbed

Elsevier and PANGAEA Take Next Step in Connecting Research Articles to Data

This is taken from Elsevier's press release:

Amsterdam, 29 July 2010 – Elsevier, a world-leading publisher of scientific, technical and medical information products and services, and PANGAEA - Publishing Network for Geoscientific & Environmental Data - today announced their next step in interconnecting the diverse elements of scientific research. Elsevier articles at ScienceDirect are now enriched with graphical information linking to associated research data sets that are deposited at PANGAEA. This enrichment functionality offers a blueprint of how Elsevier would like to work with data set repositories all over the world.

Which is very nice indeed and shows the direction which 'linking data' hopefully takes! PANGAEA now delivers a small map (iframe) which Elsevier embeds in their article pages. It shows the geographical position of supplementary data which is archived at PANGAEA. Some examples for this can be found here http://dx.doi.org/10.1016/S0304-4203(09)90045-7 or here: http://dx.doi.org/10.1016/j.marmicro.2007.02.002

The ScienceBlogs exodus and the holy land for geoblogs

Since ScienceBlogs have announced to host a Pepsi blog, Eruptions, Laelaps and Highly Allochthonous thought about leaving ScienceBlogs and are now looking for an alternative host for their blogs.

Of course there are a variety of possible hosts and many of us geobloggers use for example standard wordpress or blogger services. But in comparison with ScienceBlogs these are evil and infected with all kind of perverted blogs. I personally feel good here at blogger, however since my last Turkey visit I realised that this platform is blocked in some countries because of the many pornographic blogs there. And this stinks of course..

So where should a good geoblog go? I have also been asked if stratigraphy.net or Geoblogosphere News could offer a blogging platform. The answer is no, but maybe another purely scientific host like Nature Network would be the holy land for geoblogs?

Should I stay or should I go now..?

iGeoinfo is back

Last year we had to report on the demise of iGeoinfo, the International Coalition for Geoinformatics. At this time, the domain igeoinfo.org was taken over by domain grabbers and just too expensive to buy it back. A pitty, as iGeoinfo indeed stood for good transantlantic geoinformatics cooperation. But..there's life in the old dog yet: I recently noticed that the domain was on the market again and offered for free! I bought it, recovered some of the old contents and here it is again: http://www.igeoinfo.org.

The Geoblogosphere – A Bibliography

Lutz has collected an interesting blogospheric bibliography at geoberg.de covering 'scientific papers and important articles and projects dealing with the geoblogosphere in a more universal sense.'

Elsevier's 'article of the future' vision

Elsevier has presented their vision of the 'article of the future' at the CELL website where a short video introduces some new features for future web journals.

The first striking detail is a tabbed menu on top of the article which allows to navigate between the main sections of an article such as abstract, results, discussion etc. as well as data, figures and references. This is nothing revolutionary but a progress - currently you can only navigate between the article, the figures and the references.

Most interesting are their attempts to link as many information as possible to allow a quick overview on the essence of an article. Surely a result of Elsevier's journal XML (however they call it), which precisely describes the structure of an article and allows to mark elements such as figures or citations within the text. This linking allows interactive navigation within the article. You can immediately take a look a figure by clicking on a link within the results section. And vice versa, by clicking on the data or figures you can immediately highlight the secions in which this figure is mentioned.

However, what was intended to support 'fast reading' seems a bit confusing to me. The text, figures and figure captions are all shown at one page. As a result the area in which the text is shown is reduced to a very narrow column which makes it hard to read. Further, sometimes the figure captions seem to be shown below the figure and sometimes beneath, very confusing.

And Elsevier's idea of a graphic abstract seems really ridiculous to me. This just perverts scientific reading: Mouse eats fatty diet -> Tumor grows -> Mouse dead. Come on guys!!

I was also a bit disappointed by the way Elsevier treats data and external information sources. Elsevier's seems to regard figures as data. But figures are of course highly interpretative visualisations - based on data! It would therefore be great to be able to click on a figure and see the data on which it is based on.

Today a growing amount of such data is stored in specialised data centers such as GeneBank or PANGAEA. But from the impression the demo gave to me, linking to such external sources seems not to be the part of their vision. This is astonishing, as some very exciting and successful cooperation already exist. Just think of the already existing links to GeneBank or the recently announced cooperation with PANGAEA for geoscientific supplementary data. Instead they included some poor Excel files in their data section.

But anyway Elsevier surely heads to the right direction and most of the issues above can easily be fixed. But honestly, if presented to the audience in it's present state Elsevier's vision would offer little advantages to scientist. Most researchers would still prefer to read the abstract online to get a quick overview and print the pdfs to study the details. Or expressed as 'graphical abstract' ... see above.

Improving the Geoblogosphere's Alexa Ranking

Did you know about Alexa? It is an Amazon company which provides -among other services- a web site "traffic rank" as a measure for a web site's or blog's importance. Beneath Google's Page Rank it is one of the most influential rankings, as it is often used to estimate the "value" of a site or blog. The Rank gives the position of a web site within the popularity hierarchy of the web. That means the higher the number, the less popular your site is. Google for example has an Alexa Rank of #14..

I was a bit disappointed to discover that Geoblogosphere News' Alexa ranking was higher than 5 Mio!!. And also most geoblogs I have checked have an Alexa rank which imho does not at all reflect their real value.

To check how your or other geoblogs is ranked by Alexa, you can visit the list at Geoblogosphere News at: http://geoblogs.stratigraphy.net/?action=list. Click on the question mark icon and you will see the Alexa Ranking and other information there.
Alternatively, you can also just visit the Alexa site and enter the URL you are interested in there.

Meanwhile I discovered a website which explained how this ranking works: it is dependent on the number of users visiting your site which have the Alexa Toolbar installed! After I installed the toolbar in my browser, the ranking significantly improved..

So it seems quite easy to improve the geoblogosphere's Alexa ranking. Just install the Alexa Toolbar and simply visit geoblogs. If a number of geobloggers would do that, the geoblogosphere's Alexa ranking and overall visibility of geoblogs would significantly improve!

Lithology logs: using Psicat XML to create SVG outputs

PSICAT is a very nice tool to create lithology logs for sediment cores. One of the most interesting features of PSICAT is it's own XML export format. The format is very simple, it basically consists of two element: 'model' and 'property'. 'Model' is just a simple container for data and can represent an Interval, Bed or Lithology etc.. A 'model' can contain several 'property' elements, which represent simple key value pairs. Here is an example:

<model id="158cc6_1250de53dc5_15" parentId="1899213_1244fb3b1d8_1" type="psicat.core.interval.Interval">
<property name="depth.top">0.00</property>
<property name="depth.base">0.60</property>
<property name="grainsize.base">-1.56</property>
<property name="grainsize.top">-1.56</property>
<property name="contact.type">sharp</property>
</model>

Last week I was playing with this format and was surprised how easy to handle it was. In an attempt to do something useful with it, I tried to create an SVG (scalable vector graphics) output based on PSICAT data. And it worked! The first version is able to plot Intervals and Beds quite nice. You can try it here: http://www.stratigraphy.net/psi2svg

UPDATE: The code and tool has been moved, please visit http://www.lithologs.net !

Boring latin names are banished

This funny link just came in via the taxacom list:

Dudley UnEarthed :

On the lower floor the museum has its major interpretative displays in a recently refurbished gallery called ‘Dudley Unearthed’. The gallery features two time lines, one showing the place of the famous Silurian Geology of the area in the history of the Rocks of Britain and the other showing the place of the industrial revolution in the human history of the area.
Boring latin names are banished but if you want more information just ask !

Well... generally applied, this would solve much of our taxonomy troubles ;)

Twittering data - what to do with dit.li?

I started using twitter last year and was quite impressed by the number of tools offering extra services on top of it.

Onfortunately there is nothing out there which is suited to send data.
You can of course simply link data to tweets via a short url (e.g. tinyurl), but it is impossible for your followers to identify what's behind a shorturl before you click on it. Could be data could be anything else..

Also data dois won't work unless there is something like a short-doi as twitter will shorten doi links to tinyurls.

But wouldn't it be much cooler to have all the twittered data at one -trusted- place? Twitpic is a good example how this works for twittered images.
To mimic a service like this for data and to allow to identify twittered data, the first thing needed is an own short url.

Fortunately, I got dit.li, one of the rare, left, semi-meaningfull three letter domains and so I started some trials:
My first approach was to allow manual data entry in a textarea or *.txt file upload to save data at dit.li. I also added some nice javascript charts to display the data. The twiter API is quite simple, so it was easy to allow sign in via the twitter authentification service. Sending the data by twitter was also very easy by using the twitter API. Some example how sent looks like is : http://dit.li/018. I also started to play with data dois, so you can now also send data by just entering a data doi.

All good so far, but after having fun programming all this I lost all confidence in this project. Is it be useful to send data via twitter anyway?
Any feedback is welcome!

Paleontology in the 21st Century

Yesterday I stumbled upon a recently published paper by Wolfgang Kiessling (Natural History Museum Berlin) about the current state of paleontology in Germany.

Kiessling, W. et al., 2010. German Paleontology in the 21st Century. Palaeontologica Electronica, 13(1), 13.1.2E. (online)

In this editorial piece, Kiessling and co-authors reflect on the current state of paleontology in Germany, the reasons why paleontology has become a niche subject, despite the fact that biodiversity studies receive a lot of interest (and money), and despite the fact that paleontology used to be at the core of geology. Kiessling et al. identify a number of factors specific to the situation in Germany, but many factors that can be generalised.

The greatest risk for German paleontology is the continued closure of university departments and the replacement of retired paleontologists by non-paleontologists. This threatens the future of our students in science and the paleontological research community may fall below a critical mass which is needed for innovative research. Some of these problems fall in the responsibility of the paleontologists themselves (e.g., lack of innovative approaches, apparent absence of practical/ economic applicability, tactical mistakes) but others are the result of administrative actions to save or shift resources independent of the quality of research and teaching.

I tend to disagree with Kiessling's identification of cause and effect. (See also in Stratigraphy.net internals "Paleontology - The very late adaptors?" of 15 Feb 2008.) But I do hope, that some will perceive this paper as a wake-up call to move paleontology into the 21st Century.

MetaCarta annonces End-Of-Life of Webservices

This week I received an email from MetaCarta in which they announce the end of their generous conditions for using their web services as well as some major technology changes.

We are improving the capabilities of MetaCarta's powerful Geographic Search & Referencing Platform (GSRP).

Over the next 30 days we'll be transitioning to a new system for MetaCarta Web Services. After this transition is complete you will no longer be able to access the current OnDemand service. If you would like to sign-up for a free 30 day trial account to try our new Web Service you can do so at our developers page.

Sad news as this surely means the 'beginning of the end' of the free usage of MetaCarta's geoparser tool which I used for Geoblogosphere News to identify placenames and locations mentioned in blog posts. Fortunately, Yahoo! has released their Placemaker geoparsing Web service last autumn, so there is an alternative!

The colour of Cretaceous dinosaurs and birds

In a recent paper in Nature Fucheng Zhang and co-workers report on their work on fossil melanosomes of Cretaceous dinosaurs and birds. The examination of fossil melanosomes gives important clues to the colour of feathers or skin of these creatures. The expressive colour patters of early feathers Cretaceous dinosaurs and birds adds to the discussion whether feathers evolved first for flying, or whether they served other purposes, i.e. signalling to potential mates or rivals.

Zhang, Fucheng, Stuart L. Kearns, et al. (2010), Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds, Nature, online, doi:10.1038/nature08740.

How did dinosaurs move?

Recent advances in computer technology allowed remarkably realistic animations of dinosaurs (and other creatures) in films. But how realistic are these animations?

In a recent feature, Danielle Venton of International Science Grid This Week (iSGTW) writes:

In a memorable scene from Steven Spielberg’s Jurassic Park, a Tyrannosaurus rex gallops behind a jeep, close to overtaking it, lunging to take a bite out of Jeff Goldblum — to the horrorified delight of millions of thrill-seeking movie-goers.

Assuming dinosaurs could be resurrected, how realistic would this situation be?

Not very, according to Karl Bates, a researcher in dinosaur locomotion. In fact, our scrawny-armed, prehistoric friend would probably have trouble outrunning a bicyclist. Depending on how fast you run, you may or may not be in trouble if you were on foot.

(...)

By his best guess, this dinosaur ran at about an average running speed of 15 miles per hour (24.5 kph) and would have walked at about 5.5 mph (9 kph), faster than the average humans — but not the fastest ones.

It turns out that muscle size is the single most important determinant for dinosaur speed. Since we know little about their actual muscle mass, there is a lot of guess work involved. But with these new high-performance models it is an educated guess. The model allows to study different scenarios in a physical environment, including gravity.

Who killed Bambi? Bambiraptor!

While researching more material for my previous post on "Vertebrates and their vertebrae" I came across an intriguing name.

Who killed Bambi? Bambiraptor feinbergorum!

DinoData lists:

Bambiraptor was discovered in 1994 by 14-year-old Wes Linster, who was hunting for fossils near Montana's Glacier National Park. Now, scientists have identified it as what may be the most convincing evolutionary link yet between dinosaurs and birds: a 75 million-year-old creature with a roadrunner's body, arms that resembled clawed wings, and thin, hair-like feathers, anatomically it is the most bird-like dinosaur yet discovered.

Vertebrates and their vertebrae

Looking at modern vertebrates, their number of vertebrae varies remarkably. While some snakes have of the order of 300 vertebrae (all thoracic vertebrae), some turtles only have 18 vertebrae in total - from neck to tail. Then, in mammals the number of vertebrae and their functional division is remarkably constant.

In a recent study Johannes Müller (Berlin Natural History Museum) and co-workers surveyed 436 recent and extant amniote taxa to study the development of vertebrae in response to environmental pressure, body mass and genetic factors.

The key findings were:

• Early mammals (synapsids) had six cervical vertebrae and in total twenty thoracic plus lumbar vertebrae.
• The number of vertebrae is determined by somite formation and Hox-gene expression during embrional development. This also determines the position of the limbs along the spinal column.
  
• Early synapsids already showed the same number of vertebrae as recent mammals, while basal reptiles already showed a great variation in their number of vertebrae.

The paper is available on-line at PNAS:

Müller J., Scheyer T.M., Head J.J., Barrett P., Werneburg I., Ericson P.G.P., Pol D., Sánchez-Villagra M.R: Homeotic effects, somitogenesis and the evolution of vertebral numbers in recent and fossil amniotes. In: Proceedings of the National Academy of Sciences (PNAS), doi: 10.1073/pnas.0912622107

The paper comes with substantial amounts of supporting information. Unfortunately, the direct link from the article "splash page" does not work. This, again, shows the importance of using persistent identifiers like DOI for the publication of supplementary data.

Linking geoscientific data to journals and vice versa

A major breakthrough for data publishing was recently announced at the Aquatic Sciences News from Elsevier:

PANGAEA (the Publishing Network for Geoscientific & Environmental Data) and Elsevier introduced reciprocal linking between their respective content in earth system research. Research data sets deposited at PANGAEA will now be automatically linked to the corresponding articles in Elsevier journals - and vice versa. Through this agreement and development Elsevier supports and acknowledges the importance of long-term storage and wide availability of large research data sets. Furthermore, through this linking functionality Elsevier also introduces a proper credit mechanism to the author's research for data sets deposited in this earth system research data archive.

This effort is not a simple link exchange, but based on the consequent usage of DOIs on both sides plus some advanced, identifier brokerage services.