Sharing our Standard Operating Procedures

A lot of science is like baking – you follow a procedure (recipe) and generate a batch of data (cake). If the same sample is analysed following the same procedure in two different laboratries, the data generated should be the same. This is not always the case, but standardising the approach across a research community reduces the scope for variability between datasets and allows for comparison between studies.

In a lot of cases, protocols are generated by carefully reading the methods section of a published paper, but publications are often written very concisely and some of the steps taken in the lab could be left out or hard to follow. The step-by-step protocol is less likely to be published, but could be much more useful for those trying to build upon published studies.

To avoid that confusion, I have created a new section of the website dedicated to publishing the latest version of our laboratory standard operating procedures. These are published under a Creative Commons CC-BY 4.0 license so you are allowed – encouraged in fact – to use, adapt, improve and share these protocols.

I also welcome feedback regarding the protocols. Comments are enabled on each one and you are welcome to highlight steps that are unclear or could be improved.

#BOGS2019

I hosted the 2019 British Organic Geochemical Society conference at Manchester Met. Personally, I think it was a huge success and would like to reiterate my thanks to all of the delegates for making it a fantastic event, to the sponsors for providing the icebreaker, conference dinner, and prizes, and to the Ecology and Environment Research Centre for subsidising the conference fees. Conference abstracts are archived here.

BOGS 2020 will be hosted in Birmingham by Dr James Bendle.

Set up is underway!
Poster hall all ready to go
Icebreaker in full swing
Thank you to the sponsors for the icebreaker drinks
Poster session in full swing
Keynote presentation by Jaime Toney (image G. Inglis)
Conference dinner at Croma
Handing over the BOGS brush to Birmingham

More twitter reaction here

Ivory mining from thawing permafrost

The Guardian newspaper today reported on an interesting set of photographs today documenting one side effect of warming permafrost. Photographer Amos Chapple travelled to the East Siberian region to mine prehistoric ivory from permafrost. Locals had discovered tusks emerging from the river bank as rising temperatures coupled with erosion to uncover bones and tusks that had been buried for thousands of years.

A tusker excavates a prehistoric bone. Photo by Amos Chapple / RFE/RL
A tusker excavates a prehistoric bone. Photo by Amos Chapple / RFE/RL

The photographs are well worth a look, documenting the extreme (and extremely dangerous) lengths that the ivory miners (“tuskers”) will go in order to find ivory worth tens of thousands of dollars per piece. They carve caverns into the permafrost using high pressure hoses, leaving behind a pock-marked hillside and a river full of debris.

A successful find will net more than $50 000 in cash, and the carved products will be sold for millions, likely in China. While the payback for the few who strike lucky can be life changing, the damage to the local ecosystem, and the likely increase in permafrost degradation and carbon release due to this activity, means that the long-term regional and global consequences will far outweigh the local gain.

Greenland from the air

I was lucky recently to fly to Boston in the USA, with a connecting flight in Rekyavik, Iceland. While flying over the Eurasia-America plate boundary into Rekyavik airport was pretty impressive, with cracks in the ground visible from the plane as the continents slowly tear apart, the best part was that the route from Iceland to New England takes you over both sides of Greenland.

From the air, you can see glaciers flowing into the ocean, with bright blue meltwater lakes forming on top of the ice streams, the ice cap itself, and the slightly more inhabitable land on the western coast. It was a truly magical experience, unlike anything I’ve seen before, and a complete surprise. If you are flying Icelandair along this route in the future, make sure to sit on the right hand side of the plane to get the best views.

Ice stream on the East coast
Ice stream on the East coast

Supra-glacial lake
Supra-glacial lake

Ice stream and icebergs
Ice stream and icebergs

Supra-glacial lake
Supra-glacial lake

West Coast
West Coast

What is: Open Access publishing?

Peer review is generally accepted to be the least-worst way to generate trust in the scientific publishing process. By allowing experts in the field to read, critique, confirm, challenge and improve your work before it enters the mainstream body of science, poor quality or erroneous work should be filtered out before it gets the chance to distort public perception and policy. However, it’s not without its critics. Anonymous reviews allow reviewers to partake in spiteful and/or personal attacks which do nothing to improve the science behind the work, and can delay or even prevent publication of perfectly acceptable work. Also, the system is based on a financial system that only seems to benefit the publishing companies. In traditional journals, scientists relinquish their copyright to a company that then charges them and their colleagues to read the work, restricting access to those in universities or with big budgets (individual papers can cost $30 or more, subscriptions run to the thousands). Journal reviewers and editors work for free, considering the process as part of their community obligation despite the for-profit journal getting the real benefits.

Recently, open-access publishing has started to change the way that ordinary people can read the research that they, through their taxes and charity donations, have paid for, but the business model for the publishers is generally similar. In a typical open access publishing workflow, the researchers submitting the paper pay an “article processing charge” (APC) once the work has been accepted. Paying this charge, which is often £1000 or more, allows them to retain the copyright, and lets anyone, anywhere in the world, read the paper for free. It shifts the costs for access from the distributed consumers, who would often lack the resources to pay for the research, to the universities producing the work in the first place. Most research grant bodies now request open access publishing, and have provided some funds to cover the APCs, for now at least. Reviewers and editors are still unpaid, and publishers still make a profit, in fact since many articles are not open access then universities (i.e. taxpayers) are on the hook for both the journal subscriptions and the APCs.

So why are researchers still paying these companies such large amounts of money (profit margins are amongst the best of any industry)? Well, academic promotion is mostly decided by your publication history; the easiest way to judge a publication history is to look at the journals that a researcher publishes in, rather than reading the papers themselves. Therefore the pressure is on, especially for young researchers, to publish in the most prestigious journals, and they tend to be the most expensive ones, where articles are either restricted access or have high APCs.

Recently, there has been a shift towards more open and accountable publishing systems, with journals allowing researchers to publish either draft versions or even the finished paper on their website without violating copyright. Many universities have created online repositories to let researchers store and share their work (mine is available through my Manchester profile page), which are imperfect, since it’s often hard to find the papers, but better than nothing.

Even within my short career, the way that people publish and access science has changed; open publishing is still in development and it’s likely that further innovation in the next 5-10 years will change the landscape even further.

Canadian permafrost as a source of easily-degraded organic carbon

The February issue of “Organic Geochemistry” will include a paper by David Grewer and colleagues from the University of Toronto and Queen’s University, Canada which investigates what happens to organic carbon in the Canadian High Arctic when the surface permafrost layer slips and erodes. This is a paper that I was involved in, not as a researcher but as a reviewer, helping to make sure that published scientific research is novel, clear and correct.

Map of Cape Bounty in the Canadian High Arctic
Map of Cape Bounty in the Canadian High Arctic

The researchers visited a study site in Cape Bounty, Nunavut, to study a process known as Permafrost Active Layer Detachments (ALDs). The permafrost active layer is the top part of the soil, the metre or so that thaws and re-freezes each year. ALDs are erosion events where the thawed top layer is transported down the hillslope and towards the river. Rivers can then erode and transport the activated material downstream towards the sea.

The team used organic geochemistry and nuclear magnetic resonance spectroscopy to find out which chemicals were present in the river above and below the ALDs. The found that the sediment eroded from the ALDs contains carbon that is easily degraded and can break down in the river, releasing CO2 to the atmosphere and providing food for bacteria and other micro-organisms in the water.

Arctic sea ice over one year

As 2014 draws to a close, what were the key features of the Arctic climate this year? Today let’s look at the sea ice coverage. The US National Snow and Ice Data Centre has a monthly running commentary on ice cover on their website, and in general 2014 has been “extremely ordinary”, by which they mean that sea ice grew and shrank at roughly the rates of the last few years. Ice cover was not as low as 2012, the record-breaking year for sea ice retreat, instead it was pretty average for recent times. Remember that this is still way down on the long-term average.

Monthly Arctic sea ice cover for the last few years (NSIDC)
Monthly Arctic sea ice cover for the last few years (NSIDC)

Using their monthly data, here is an animation of the sea ice changes over the last 12 months. It’s a reminder of just how dynamic the Arctic is. Sea ice cover is important for a number of reasons. First of all, the white colour reflects sunlight that shines onto the ice surface during the summer. Reflecting sunlight back into space means that it does not stay around to warm our planet, so having a decent covering of ice helps to regulate temperatures. As the summer sea ice cover has decreased in recent years, the amount of sunlight reflected back into space has decreased, meaning that there is a positive temperature feedback at work here.

animsm
Arctic sea ice cover over the last year

Sea ice cover is also important for the Arctic Ocean’s biological cycle. Many plankton require sunlight for photosynthesis, so the retreat of sea ice during the spring and summer causes a bloom in biological productivity in the surface ocean which feeds down the food chain, supporting large numbers of fish and whales. As organic geochemists, we can see this plankton bloom by looking in the ocean sediments biomarkers. There are specific chemicals that are produced by marine organisms that can be used to track the productivity, and it seems that there is a direct link between the ice-free areas and the highest amount of biological activity.

Manchester Museum – Siberia Exhibition

Starting this Saturday 4th October, and lasting until 1st March, the Manchester Museum will be holding a special exhibition on Siberia. This will contain a collection of special items from British and Russian museums, including a mummified baby mammoth and a brown bear, along with displays on the culture and natural history of the region, taking visitors beyond the stereotypical view of Siberia as an icy wasteland. Along with colleagues in Manchester, Newcastle and London, I have made a display board and video about Siberian climate change, which will be showing throughout the exhibition. More to follow once the exhibition opens…

Official Museum Poster

US Government review of climate change

This week the US government released their own review of the climate, including the current state of play and predictions for the future. They conclude that climate change is happening now, affecting lives today, and not just something to worry about 20+ years in the future.

 

Modelled temperatures with and without human CO2 emissions
Modelled temperatures with and without human CO2 emissions

The report website is very comprehensive and well-written, and I’m not going to reproduce it here. The section on Alaska, complete with interactive photos and charts, is relevant to permafrost research across the whole northern hemisphere.

 

What Is: GRAR?

Russia is big, really big, and to go with that, it has some very big rivers. The majority of the Russian river outflow is into the Arctic Ocean, especially in the central and eastern parts of the country, and this is generally concentrated into a series of very large rivers. The largest of these are known as the Great Russian Arctic Rivers (GRARs). From west to east, these are the Ob, Yenisety, Lena, Indigirka and Kolyma, of which the Ob and Lena are largest, and Indigirka the smallest (small enough to not count in some people’s list of GRARs).

Catchment areas of the Great Russian Arctic Rivers
Catchment areas of the Great Russian Arctic Rivers

The Ob river is the world’s fifth-longest and has the sixth-largest drainage basin, yet has only the 19th highest annual discharge, being overtaken by the smaller Yenisey and Lena rivers to the east of it. All of these river basins contain some permafrosted land, which can reduce discharge during the winter months and have a very large flood-period in late spring / early summer when the meltwater arrives (the “freshet”).

Permafrost within catchments of the GRARs
Permafrost within catchments of the GRARs

As the amount and continuity of permafrost increases from west to east, so the proportion of each permafrost type increases within the river basin. The Ob and Yenisey are largely free of continuous permafrost, allowing water to flow through the ground to the bedrock and into the river, whilst the Indigirka and Kolyma are practically 100% continuous permafrost, and thus any water discharging will have run along the top of the ground before entering the river itself. This can have consequences for the type of material, especially carbon, carried by the rivers.

Proportion of each type of permafrost within river basins
Proportion of each type of permafrost within river basins

This east-west contrast is worth exploring in more detail in a later post, since it shows how Siberia may behave very differently if the permafrost were to thaw. As a final reminder of just how large the rivers are, even the smallest, Indigirka, manages to cover more area than the British Isles! As usual the full-resolution PDFs of the figures from this article can be downloaded here: River catchments no permafrost, Catchments and permafrost, Permafrost chart, Catchments and UK.

Comparing the catchment areas to the British Isles
Comparing the catchment areas to the British Isles