Sources of open access scientific papers

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We are all used to open access to information on the Internet, but when it comes to scientific papers, for most people a barrier comes down. However it is possible to find publicly accessible copies of scientific papers available right now.

I’m building up a list of sites as I find them, as I will use them in my blogging. I’m focussing on Geosciences but many sites are not subject specific. Please make use and if you know of any others, let me know via the comments. I’ll add them to the main text over time.

Caveats – A lot of these sites don’t have a massive amount of content. Some list papers but have no publicly available copy. Often the copies are ‘pre-publication drafts’ with odd formatting. All sites have terms of use that you probably read, definitely if you want to do anything but read them.

Usage – Most of these are repositories for organisations. If the primary author of a paper you know of is at one of these institutions then its worth a look. At least some of them are Google searched, in which case that is your best route if you are looking for a specific paper. Either way, don’t assume a recent paper can only be found via the journal.

In descending order of usefullness:

http://nora.nerc.ac.uk/ is a repository for papers produced by UK government agencies, for my purposes the British Geological Survey and British Antarctic Survey. Coverage sketchy before 2010 but good thereafter.

http://www.geosociety.org/gsatoday/ All of the GSA’s “GSA Today” are available online and they are keen for bloggers to refer to them.

Open source journals may be the future? EGU has a selection: http://www.egu.eu/publications/open-access-journals.html (thanks Bill).  The Solid Earth journal is the one that most caught my eye.

 

http://oro.open.ac.uk is a repository for the UK Open University. Seems to list all papers since 2009 and about 30-40% have text.

http://dspace.mit.edu MIT seems to have very good coverage.

http://eprints.whiterose.ac.uk is pretty good coverage.

Poikiloblastic in the comments has useful stuff about planetary science articles and lists of Open Access Journals.

John Stevenson, aka volcan01010 my blog-neighbour, points me to http://www.pubvolc.net/ which is a rather smart idea. It is a volcanology literature database that allows you to contact the author for a reprint.

http://wiredspace.wits.ac.za/ appears to be just MSc/PhD theses at Wits University in South Africa.

http://earth.usc.edu/~jplatt/Publications.html  only papers by John Platt, but each one a gem!

http://ora.ouls.ox.ac.uk/ is a repository for Oxford University and http://www.dspace.cam.ac.uk/ the same for Cambridge. Coverage of geoscience is pretty poor. Oxford is apparently digitising all of its theses, even the old paper ones, which is rather pleasing to me since I wrote one of them.

 

Crème brûlée or jelly sandwich?

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This post is part of my journey into the geology of mountains.

Rocks can behave rigidly, or under some conditions, they are ductile and can flow. This is a remarkable thing, which helps explain why the theory of Continental Drift was not more widely accepted (prior to the plate tectonic revolution of the 1950s). Seismic evidence from the deep earth shows that the crust and mantle rocks behave elastically (on short timescales). This was taken as evidence that they could never flow, meaning the continents couldn’t drift. We now know that hot rocks in the mantle can flow (over long timescales) and that this is a necessary part of plate tectonics.

What about other geological implications? What other things can be explained by the ‘Jekyll and Hyde’ way in which rocks deal with stress?

Small scale structures: Most rocks under surface conditions behave rigidly – they only change their shape by fracturing or by being dissolved. Rocks deformed near the surface are therefore typically fractured or faulted. Slightly hotter rocks may be deformed by dissolution, where material is dissolved into solution and redistributed into veins. Stylolites and cleavage are structures formed in this way that are common in deformed sediments. Salt and mud and are two substances that can flow in cold shallow rocks. Salt diapirs and mud volcanoes are structures where these light substances flow towards the surface.

Stylolite from Ron Schott on Flickr (http://www.flickr.com/photos/22644739@N00/4468019786)

To deform typical rocks in a ductile way, they need to be under conditions associated with metamorphism – below depths of about 15-25 km and above temperatures of ca. 300 oC.

Under these conditions, various forms of sold-state creep begin to work and rocks can ‘flow’. Typical structures here are fabrics, such as schistosity or gneissosity – entire rocks are deformed as shown by the flattened minerals within them. Often there are areas of very high strain called shear zones, typically containing mylonites. A process called strain softening, plus perhaps a focussing of water or heat flow makes these zones softer than the surrounding rocks, meaning that they get more and more deformed.

Shear zones are analogous to faults, indeed a major structure may be a fault near the surface but a shear-zone at depth. A shear-zone is likely to be wider than the equivalent fault – the deformation is distributed through a large volume of rock.

Shear zone in amphibolite from Ian Stimpson @hypocentre (http://www.flickr.com/photos/17907935@N00/6723121739)

What controls the brittle-ductile transition? Major controls on the rheology of rocks are  composition, temperature, pressure, the presence of liquid, and the presence of melt. Composition is quite hard to change, but if you increase any of the other things, the rock is more likely to behave in a ductile fashion.

Large scale features, large scale evidence. There are some big features that can  be explained in terms of their rheology, which means they can be used to directly measure the rheological properties of the crust.

Foreland basins are sedimentary basins where the accommodation space (the hole in the ground filling up with sediment) is created by the flexure of the rigid upper crust.  Think of the Indian continent being pushed under the Himalayas and Tibet.  The weight of Tibet is pushing down on the Indian plate and this bends it downwards. The space created fills with sediment being eroded from the Himalayas. The Ganges basin is formed.

The Indian crust is cold and rigid. Clever folk can do the maths on the shape of the crust as it bends down. This confirms that the pattern matches the model for rigid, elastic deformation. It also allows then to calculate the plate’s flexural rigidity, which is a measure of its strength. This means quantifying the rheology of real bits of the earth, which is a very useful trick.

If you read up more on foreland basins, the picture gets more complicated as, over time the crust will further deform in a viscous way. I want to take you away to a different example of viscous behaviour.

There are raised beaches all over high-latitude areas of the Northern hemisphere. These are fossil beach deposits now found metres above sea-level. They can’t be explained by global sea-level changes as equivalent features are not found further south.

Raised beach from Scotland (in foreground). From SAGT @http://www.flickr.com/photos/sagt/4304338029/

These raised beaches formed when global sea-level was similar to today’s level: they are raised because the earth’s surface has risen up since they were formed. This isn’t due to tectonics – these areas are far from any plate boundary. What these areas have in common is that they were covered with kilometres of ice during the last ice age. This ice weighed a lot and this force pushed the crust down. The upper crust bended rigidly, pushing underlying viscous rocks (probably in the mantle) out of the way. The ice melted relatively quickly, removing the downward force. The viscous mantle rocks are slowly recovering, flowing back into glaciated areas and lifting the earth’s surface, leaving fossil beaches high and dry. The overlying rocks are being passively pushed up, with occasional post-glacial earthquakes occurring in otherwise tectonically quiescent areas. Once again, these natural phenomena are an excellent opportunity to directly measure the physical properties of the earth’s interior: the rate of rise lets you measure the viscosity.

Crème brûlée versus jelly sandwich

So the earth is strong near the top and weaker at deeper levels? If so, it would be like a crème brûlée. A giant spoon digging into the earth would crack through an upper layer (like burnt sugar in a crème brûlée) and then scoop gently through the soft mantle beneath (creamy custard).

If the earth were boringly simple, this would be accurate, but as you know, life is more interesting than that. The earth gets hotter with depth, so rock is more likely to be weaker with depth, but the composition of the earth is not constant. It’s long been known that the surface layer that moves as part of plate tectonics (the lithosphere) is not just the crust. There is a layer of mantle material (lithospheric mantle) stuck to the bottom of the crust meaning that within the lithosphere, there is a dramatic compositional change which complicates matters.

An interesting paper by E.B. Burov and Tony Watts (available here, thanks GSA!) discusses the crème brûlée model and compares it with a ‘jelly sandwich’ model. A jelly (jam) sandwich has a soft layer between two stronger layers. The sandwich model supposes a strong rigid upper crust, a weak hot lower crust  and then a strong layer of lithospheric mantle.

You’d have thought that, knowing the composition of average crust and mantle and the conditions with depth, we could resolve this debate easily. As it turns out, although we know that olivine-rich mantle is much stronger than quartz-rich crust we don’t know by how much. It is very hard to run experiments with low strain rates and high temperatures comparable to real-life conditions so we can’t measure directly.

Burov and Watts combine numerical modelling and indirect observations to settle the issue. Think back to the Indian crust subducting under Tibet. One of the things you can infer from geophysical studies of these situations is the effective elastic thickness of the lithosphere. This is the cumulative thickness of rocks that are behaving elastically. For India, this is 70km, which is greater than the thickness of the crust. This is hard to explain, unless the lithospheric mantle is strong, suggesting you have a thick sandwich, not a thin layer of burnt sugar. They also show numerical modelling that suggests that without a strong lithospheric mantle, subduction and mountain building wouldn’t be possible.

Note that for this last section I’ve switched to talking about weak/strong rather than rigid/ductile. If you a simple sort like me, you can think of the two as synonymous, but they are not really which is why Watts and Burov talk about long-term strength. Complications arise because most rocks are viscoelastic – they transmit earthquake waves elastically (over short timescales) but behave viscously over longer timescales. The paper gives you a taste of this, but I’m not the man to take you any further into that world.

Rocks behave in complicated ways when placed under stress. I hope I’ve given a taste of the complications that arise from this in the wider world. I leave you with one thought: if you squeeze an over-filled sandwich – what happens to the filling? I will return to this and how it relates to Tibet and the Himalayas, in another post.

Accretionary Wedge #44 – “most important teacher”

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Teaching is not just about imparting knowledge. To quote Elli Goeke, an important teacher is a “person has influenced not just my knowledge of a particular subject, but has also changed how I address research or teaching or just life in general (or all three).” These posts will teach you that great teachers can also inspire, instil discipline and generate self-belief. Denise Tang knows a Chinese expression that sums it up: teachers “pass the knowledge and good traditions to the next generation”.

We’ll start with Southern Geologist’s first contribution to an accretionary wedge, on a new blog. The post describes a inspirational introductory course in Geology, which for variety and interest put other sciences in the shade.

Short Geologist picks an anonymous college chemistry teacher whose good teaching cured a phobia of ‘hard’ equation-rich subjects and laid the foundations for successful geological studies.

Denise Tang over at Life as a Geologist owes a debt to Prof. LS Chan, who introduced her to Geology and so “passed the flame”.

My post on John Dewey describes how I learnt the importance of breadth from a remarkable man.

John Adams (the Geologist) was taught geology by not one, not two, but three Ulstermen called Reid and is interested in knowing if anyone else remembers them.

Over at Life in Plane Light, Elli Goeke tells us about three ‘runner-up’ teachers  but settles for Kim Hannula as her most important, someone who is a mentor as well as a teacher.

Hollis over at Plants and Rocks gives us a tribute describing the life and work of Dr Brainerd “Nip” Mears Jr, a man who contributed to our understanding of the Geomorphology of the American west, but who put his students first.

Following a common theme, Casey at Gioscience lists the teachers (at University of North Carolina at Wilmington) who led him to a love of Geology: Dr. W. Burleigh Harris, Dr. David Blake and Dr. Michael Smith.

Moving away from formal education, Dana Hunter offers a characteristically engaging and generously-illustrated story  (also here) about how Lockwood DeWitt fed her geology addiction with a first opportunity to “see some stuff with an actual geologist”. There are some great descriptions of what being taught by a great teacher is like and how they build confidence as well as impart knowledge.

The man himself, Lockwood DeWitt submits a touching eulogy to Harold “Sharkey” Enlows the College teacher “who made me work the hardest, and from whom I learned the most”.

Ann over solved the difficult problem of picking between her university geology teachers by talking instead about an important school teacher, Miss Relic who through belief and encouragement changed for the better the way Ann thought about learning and her own abilities.

Ryan Jackson over at Educated Erosion had no problem choosing Coach Ford, an inspiring High School teacher who set him off on a rocky road.

The next wedge is hosted by Denise Tang and is “Geological Pilgrimage – the sacred geological place that you must visit at least once in your lifetime “. Get thinking…

Granitic gorgeosity in the high Himalaya

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I’ve been writing a lot of rather ambitious wordy posts about Himalayan geology (perhaps too many, too ambitious) so I thought I’d give you a post with visual impact for a change. I can’t resist some words of explanation but I hope the pictures would speak for themselves, if I let them.

I’ve some pictures from the Indian Himalaya. I’ve put a satellite image of the area up in WoGE #322 and talked about growing a beard while here already.

Trekking in the Himalaya, you get used to amazing views. But this was a taste of something special – Gumbaranjon peak, approached from the south.

The main buff-coloured cliff face is granite, with dark layers of xenolith. The green/purple rocks on the right skyline are behind, on the other side of a major extensional detachment (in the heart of a compressional orogeny).

Walking closer and around the base, we get a better view. The dark xenoliths and light granite make it a bit like looking at a negative photo. The eye tries to trace the pattern of granite intrusion by putting patterns into the places where the xenoliths aren’t. There are hints here that the intrusion process wasn’t simple.

That’s a fold of granite in a xenolith! It looks like there must be deformation active during the intrusion process. An early dyke has been folded and now sits in a xenolith surrounded by granite. It is very unwise to infer strain from a fold (if you don’t know the initial orientation), but its interesting that the nearly extensional structure is top to the north, which corresponds to a top to the left sense of shear in this photo.

Looking at the rocks at the base on the cliff gives more evidence of syntectonic intrusion.

The central block shows undeformed tourmaline muscovite granite sitting in a triangular space within metamorphic rocks. The shape looks like a ‘strain shadow’ around porphyroclasts in a mylonite.

All good things come to an end, but as we walked away from Gumbarajon it showed us its most majestic profile.

Click for more information on the Geology of this area.