Friday, 31 May 2013

Are we approaching the dawn of continuous biodiversity data?

With technology becoming ever cheaper and more powerful, a movement to open hardware and increasing application in other disciplines, are we heading for a continuous stream of biodiversity data?

The stage does seem to be set to make use of technological advances. Three main elements may have contributed: 1) there is a well established movement towards ecosystem and community level assessments at the policy level; 2) there is an ever increasing need and gap for real time data to make informed policy, planning and management decisions; and 3) governments and monitoring authorities are predisposed to finding ever increasing ways to be resource efficient.

This type of approach is beginning to be used for other environmental data needs. One such project, currently looking for Kickstarter funding to develop further, is the Smart Citizen1 project. The aim is that through cheap hardware, citizens will deploy environmental monitoring devices across the globe. Collected data will then be sent to online platforms for viewing, analysis and sharing.

Another project, which also received funding through the Kickstarter platform, is the Protei2 sailing robot. Originally designed in response to the Gulf of Mexico oil spill, the hope of the team behind it is application in fisheries, natural reserve, coral reef and algal bloom monitoring.

Interestingly, both the Protei and Smart Citizen projects have adopted an open hardware philosophy. Essentially meaning that anyone and everyone has access to plans and detailed specifications for project hardware. Facilitating others to view and innovate using existing advancements and knowledge.

There have been developments in the area of biodiversity citizen science. However these have relied on making human collection of data more accessible to all citizens. Now and in the future we have a chance to develop continuous data streams, helping us fill knowledge gaps and tackle some of the biggest biodiversity challenges we all face.

Our team are currently working with partners on some of the many elements needed to make this concept a reality. However, there is lots still left to do, and we are always in talking to potential researchers and organisations to collaborate with and help drive innovation.

1 (Smart Citizen) -

Under Creative Commons Licence -

Friday, 24 May 2013

Will the advent of open online data publishing lead to advances in science?

Having platforms available for publishing quality scientific data, whatever the discipline is clearly a good first step. But in order to truly advance science, do we need a wealth of multi-disciplinary data, which is easily cross linked and reused.

Three particular open data sources come to my mind, although I am sure there are more. These are DRYAD, figshare and Global Biodiversity Information Platform (GBIF). Each of the three is different, leading to the potential problems of data silos being created and overlapping and splitting of scientists between platforms. However, wherever you choose to publish your data, the principles of quality data remain the same.

What would be useful, if not already available is a super platform which brings together access to all these online datasets, wherever they are. That way data could easily be gathered from cross disciplines and a range of scientists within each discipline.

Do you currently publish data online? If so where, and why? Are there any tools that would help the reuse and finding data?


NASA Goddard Photo and Video, Creative Commons 2.0 -

Friday, 17 May 2013

Can we beat the extinction rate to name all species?

Do we have the capability to name all the species on the planet before they go extinct?

Recent research1 argues that we can. Essentially we might have convinced ourselves unnecessarily that the barriers are too high. Take the commonly held belief that the number of taxonomists is decreasing. The research1 points to the increase in taxonomic data being published in repositories (e.g. WoRMS) as a sign that taxonomic output is in fact increasing.

Are we in the most productive taxonomic era ever? This argument seems to supported by the recent announcement that the Pensoft publication Zookeys reached its 300th issue recently. Adding over 100 issues in the last year alone.

The research1 also points to the fact that the extinction rate is poorly quantified and that the number of species is over exaggerated. Resulting in underestimation of the time available and overestimation of the number of species left.

Potential issues surrounding accurate prediction of the number of species are highlighted in research2 looking at species which have only been described once or ‘Oncers’. The research2 reports that these species are indicative of: 1) endemism; 2) being constrained to narrow niches; 3) poor practices during re-identification; and 4) original descriptions remain unknown. The research2 found that the number of species within the genus Gymmodinium was likely to be 234 and not 268 as previously thought.

One thing is for certain, technology and infrastructure, through the hard work of certain groups and researchers are playing a huge role in facilitating the effort to describe all species before they go extinct.


NASA Goddard Photo (Creative Commons Licence) -

Friday, 10 May 2013

The role of DNA in addressing our biggest ecological challenges

Addressing some of the biggest ecological challenges we all face, require knowing what species we have in the first place. Although not a new concept, can DNA techniques play an important role in future? Or are they just a novel concept?

An international research project1 has used DNA techniques to describe five new species of lichen forming fungi from what was phenotypically a single species. The results of such studies (i.e. unique DNA barcodes) provide a unique way to identify different species outside of traditional taxonomy.

 In order to be truly useful in closing the species information gap, infrastructure must be in place, both internally within an organisation (e.g. equipment and software) and externally (e.g. DNA barcode repositories). Although data repositories, such as GenBank and MarBOL are well established, are other aspects available in widely accessible formats?

What are your thoughts?


Pellaea under Creative Commons Licence (

Friday, 3 May 2013

Marine Biodiversity Offsetting: Is our marine data up to the challenge?

A report1 commissioned by the Crown Estates in the UK, has scoped the potential for adopting biodiversity offsetting within the UK marine environment. But even in such a well studied place as the UK, is the available data up to the challenge?

The scoping report1 specifically identifies a number of key issues and challenges which would need to be addressed to successfully establish biodiversity offsetting in the UK marine environment. One challenge being to overcome the availability of accurate and recent biodiversity information. Specifically it is the relationships between biodiversity and physical environment (i.e. biotope mapping) and at a finer scale the need for biodiversity community and ecosystem relationships. Although some mapping and data exists, this is a mixture of known and extrapolated information at the broader scale.

Coincidentally, a research article2 looked at a ‘Decadal view of biodiversity informatics: challenges and priorities’. This study looked at the continued development of this field in facilitating decision making (e.g. policy, environmental change, land-use and ecosystem services). It came up with twelve recommendations for the next decade, essentially moving towards a biodiversity systems approach to our understanding.

If biodiversity offsetting in the marine environment is to be successfully implemented (i.e. the creation of long term viable offsets), then surely biodiversity informatics must play a vital role. Specifically by helping to capture the complexity of life and its relationships on a system rather than individual level.

However, we would not be in a position to contemplate biodiversity offsetting at this stage without the progress made by the informatics community during the past decade. Huge strides have been made in creating taxonomic, metadata and semantic frameworks and infrastructure with which to facilitate sharing of accurate and quality data. Although as the research article2 suggests there is a need to tackle not only new data, but also increasing use of existing technologies and then exploiting technologies in novel ways.

In the short term it appears from at least the data point of view, there are still some challenges to address in successfully applying biodiversity offsetting in the UK marine environment. It is only through undertaking such scoping1 and broad scale assessments2 that we can begin to join the pieces of the jigsaw together and ensure efficiency in achieving the best outcomes. We just need to make sure that someone is actually putting the jigsaw together.



NOAA's National Ocean Service Flickr Photos ( - Attribution 2.0 Generic Creative Commons Licence