South Africa says: No Fracking Way!

There has been recent outrage in South Africa about plans by Shell to extract large gas reserves in South Africa's Karoo region (see e.g. this link). The Karoo is the semi-arid central basin that occupies a large proportion of South Africa's area. It is not one of the country's best-known areas; however, it is THE place to see the African starry night, catch a breath of fresh air and view the aardwolf and bat-eared fox roam. Due to the dry climate of the region, communities and agriculture in this region are largely dependent on ground water reserves for their needs. However, it is feared that 'fracking', the method proposed for extracting the gas, may contaminate the precious water supplies of the region. As a matter of fact, according to the above article, "a moratorium on the gas-extraction technique has been imposed by at least 160 communities in the US, as well as in the United Kingdom, France, Germany and Canada's Quebec province" due to its polluting potential.

I find it very concerning that obvious irregularities have characterized the mandatory environmental impact assessment (EIA) and public involvement processes of Shell's application. Once again, it appears that money has been used to bypass the environmental laws in South Africa. Mining companies are prospecting across the country, and have tried, and in some cases, succeeded in destroying (sometimes illegally) some of South Africa's most sensitive ecosystems and historical sites. And, in many cases, the Department of Mineral Affairs is allowing them to mine despite sensitive ecosystems, incomplete EIAs, potential dangers to the peoples of the region. However, NO exceptions should be permitted - stick to the laws, enforce the laws! They are there for a GOOD reason - to protect our history, our people, our resources beyond the 30 year life span of mines!

MaxEnt - made understandable

I read the recent paper by Elith et al. 2011 (appropriately titled "A statistical explanation of MaxEnt for ecologists") this weekend. MaxEnt has frequently been called a 'Black Box', and sometimes been criticized on this account, although it has been shown to perform as one of the best species distribution modelling techniques currently available. Elith and colleagues have done a great job of providing users of the software with a 'candle' to shed some light into the black box of MaxEnt. Several useful features have also been added to the MaxEnt interface, giving users greater control of several features, such as the background points that can be selected. This paper will be a good guideline for all MaxEnt users.

The potential of herbarium specimens

My undergrad training was very ecology-oriented (and zoological.) I therefore never visited a herbarium during my undergrad training, and never realized what its purpose was. Having now spent several months going through herbarium records - and databases of such records - I have realized what a wealth of information is stored in these collections. Not only are plant specimens conserved here, where they can always be revisited, but there is a wealth of information on herbarium labels that can be used for a variety of purposes. Indeed, Pyke et al. (2010) have shown that herbarium specimens have increasingly been utilized by the scientific community in recent years, and new uses for them are continuously being found. I am becoming an ever greater advocate of conserving these institutions, their data, and the continued existence of the field of taxonomy, which is essential for the basic purpose of describing and identifying species, the biological entities most frequently used in describing diversity and making conservation recommendations.

Pyke, G.H. & Ehrlich, P.R. (2010) Biological collections and ecological/environmental research: A review, some observations and a look to the future. Biological Reviews, 85, 247-266

IBS Conference - more than good food and raki!

I again had the privilege of attending the conference of the International Biogeography Society, this time in Crete, in January, 2011. This was my third IBS conference, and I found it especially interesting to observe how the field of biogeography has been advancing, and how the ideas that were presented at the previous conference have been explored in greater depth, and deeper insights into these topics have been gained. I particularly enjoyed the "Biogeography and Ecology: Two Lenses in One Telescope" seesion. The speakers attempted to bring community and macroecology together and the highlighted challenges herein. What also came out at the conference was the fact that the use of phylogenetic methods have become invaluable in advancing our understanding of biogeographic processes and patterns by also taking evolutionary processes into account, though these methods hold their own challenges, as they are often based on their own assumptions. I look forward to seeing what progress will have been made on these topics when the next conference takes place in Miami in 2013.

Forest Reserve - going, going, gone?

Yesterday, I came across the satellite image of Mucheve Forest Reserve in Mozambique. The boundaries of this park are clearly visible from space - due to the heavy degradation WITHIN its borders! It really is a sad sight to see - it appears that little of the forest remains.

I have been attending the final conference of the SUN (Sustainable Use of Natural Vegetation in West Africa) Project in Benin. This EU-funded project has been a collaboration between partners from four West African countries (Benin, Burkina Faso, Niger and Senegal) and two European countries (Denmark and Germany) and spans several disciplines. It has been great to see how the partners from different countries and different disciplines have been collaborating across country and disciplinary borders, and how this is has strengthened the science that has been produced. It can confidently be said that everyone who has taken an active involvement in the project has gained a great deal of from it.

Inevitably, this has made me think about South African science in a continental context. I know that there are some efforts from within South Africa to work within a greater African framework (and I don't just mean "doing research in another country", but actively collaborating), but it is not common. (In fact, I have heard several non-African scientists working in Africa make tongue-in-cheek remarks about how the understanding of "how the environment works" of South African scientists seems to stop at the country's borders.) Sadly, I have also heard African scientists commenting about how they are treated with some inferiority by some (and I by no means want to imply all) of their South African peers. Whether this is a result of South Africa's history, because of the ignorance of South Africans about the rest of Africa (which, admittedly, is still a dark continent to many of us) or because of the attitude of a country that considers itself to be the most developed amongst its African counterparts, this is a great shame. I increasingly realise how South African science could be strengthened by the expertise of its neighbours, and how it could also contribute to the advancement of science in other African nations. Perhaps it's the "we have to prove that we can compete on an international level" attitude of South Africans, but possibly also the source of much funding in the country (often from within the country) which have prevented much collaboration of biologists across its borders. It would be great if South Africans research would look not only at its far-northern, but also its closer northern counterparts in seeking out collaborative ventures.

Reflections

Today I am finishing off my two-month stint at Kew Herbarium, where I databased herbarium specimens of African acacias. This will form part of a project modelling the distribution of the group across the entire continent. I have been lucky enough to have received data from several other sources, which will allow me to conduct a thorough assessmnet of this widespread group across the entire continent. All in all it has been a productive time, which involved me going through virtually all of the herbarium's collections for Acacia (and some of those of the Natural History Museum). On Sunday I fly on to Portugal to supplement my data with material from Coimbra and Lisbon herbaria to fill some of the geographical gaps in the existing material I have. And then, in the not too distant future, I hope that the data will be in a workable format so that I can start running some meaningful analyses.

Acacias of Zimbabwe

I have been making increasing use of the book Field Guide to the Acacias of Zimbabwe (cbc Publishing, 1999) by Jonathan Timberlake, Christopher Fagg and Richard Barnes. In my (admittedly somewhat limited) experience of field guides, this book stands out for its excellent writing, inclusion of extra bits of information relating to the ecology and uses of acacias in Zimbabwe, good locality maps and clear drawings. Although the geographic focus of the book is mainly Zimbabwe, the authors have brought some of their wider knowledge of African acacias into the text, making the book a valuable reference work. Unfortunately, it appears to be out of print. (I was fortunate to obtain a copy from one of the authors - there may be more in circulation.)

London Rendevouz

Since I am spending two months in London (or Kew - which is only barely London), I am trying to take the opportunity of making use of the incredible variety of offers in the city. Last week I attended a talk by the Linnean Society of London, the world's oldest biological society. After rushing there after work, I arrived somewhat late (I walked in the wrong direction when I got out the underground station - this seems to happen to me regularly when I arrive at stations I haven't been to before!)... I was immediately impressed by the imposing building and the portraits of great scientists that walked the halls of the society decades and centuries ago. It therefore came as a bit of a disappointment when the presentation about Blakiston and his travels and 'discovery' of Blakiston's line - a biogeographical barrier between two the Japanese islands of Hokkaido and Honshu (same concept as Wallace's Line) ended up being more of a presentation about whom Blakiston met on his travels and with whom these acquaintances and friends of his were related/connected/befriended.
Tonight, however, I thoroughly enjoyed the Nature Live feature at London's Natural History Museum. It's a great initiative for the public to find out about the science at the museum, meet its staff, ask questions, and learn something new. Tonight's session was about how DNA extraction from museum specimens can aid us in our understanding of their present vs. past diversity. A panel of four scientists gave examples of how they use museum information in understanding the changes in populations of specific species, and also aiding the conservation of these species. Amongst the topics brought up was the Save the Tasmanian Devil project, which is sequencing the entire genome of the Tasmanian devils and employing genetics to ensure that captive breeding programmes ensure that the highest possible genetic diversity of the Tasmanian devils remains. These animals are being severely threatened by a cancer that is being transmitted through biting, and has so far proven lethal in every case. The global amphibian decline was also discussed in interesting detail. It was mentioned that in the last 30 or so years, approximately half of the worlds amphibians have been described. Unfortunately, several of these have already gone extinct, or are on the brink of extinction. It makes one wonder how many species of amphibians will quietly disappear without anybody noticing...

Someone sent me this link some weeks ago.

http://www.grist.org/i/assets/2/humble-oil.jpg

The website where this was posted states:

"From a sharp-eyed reader comes this ad for Humble Oil (which later merged with Standard to become, yes, Exxon). It may win the All Time Millenial Award for Maximal Irony. It’s from a 1962 edition of Life Magazine, available on Google Books"

Carbon Maps

I have been looking for a global/African map of carbon storage, and managed to locate two maps that are available. However, both lack accuracy to some degree or other. Another better-looking, but preliminary map was recently printed in Nature. Unfortunately I haven't been able to get hold of the underlying data. Other than that I am well on track with the work here in Stellenbosch.

Visit to South Africa

After the Christmas holidays I will be spending a month in the lab of Belinda Reyers at the CSIR in Stellenbosch, South Africa, where I hope to model the potential for carbon sequestration across the African continent. I hope to gain much from the visit - it sounds like their group is doing a lot of work that relates to my proposed project.

Finished

...literally and figuratively. I handed in my 99-page half-way report this afternoon. It was a good exercise in reflecting on what I had done in the last 17 months of my PhD, and where I'm going the last 19. I realize that I have learnt many skills since my start here and that I have gained much from the courses and experience of my colleagues. On the other hand, I also feel like I haven't managed as much as what I'd hoped to have done by now, and I hope to be able to make up for some of that at least in part in the next part of my PhD.
However, for now I'm exhausted and looking forward to not getting home from work at 11pm every night, and, in the not-so-distant future, a holiday in (hopefully) sunny South Africa.

While preparing for my half-way examination I have been reading up about Clean Development Mechanisms (CDMs), particularly in Africa. It's a little disappointing that many of these projects involve planting plantations of exotic eucalypts on large tracts of natural grassland (Jindal et al. 2009). That's just one more reason for me to think that putting a price on carbon isn't such a good idea; it just seems like one evil replacing the other. Having grown up in an area which had largely been transformed from grasslands to monospecific plantations, which harboured very few of the indigenous species and caused many of the streams in the region to almost dry out, I cannot see how these can be considered instruments to 'save the environment'.

I have been reading much about the distribution of African vegetation types - particularly what determines their distribution. It is interesting to go back to the 'old' literature, and discover how people with field knowledge only made the same generalizations that we find today with data obtained using advanced remote sensing techniques, which, in principle, allow us to find statistical relationships without ever putting our foot on the continent. In particular, I am impressed by that seminal work: Frank White's vegetation map of Africa. How one man could have gained an overview of the vegetation of this enormous, and often difficult to travel in, continent, is incredible! On the other hand, eventhough I am working with large-scale datasets, I find that knowing some parts of Africa is immensely helpful for interpreting the patterns I find. I do have to be careful, however, that my interpretation of the results I am obtaining for my studies is not biased towards what I know of southern African (and the little I saw of West African) ecology? I should plan a trip to East Africa soon, I think! :)

A late-night entry

Despite mounting pressure, and days when I feel like my PhD might implode (I hope I'm not the only one who has days like this), this week has been good. Increasingly I have more direction for the upcoming projects and I look forward to the legume project, which seems to be taking off. I am excited about the collaboration with the legume group at Kew, which, I am sure, will be inspirational and interesting. And, of course, I look forward to spending some time in London - I love the city (and everyone speaks a language I understand)! Let's hope it'll all work out.

fun at the museum

I remember how, as a little girl, I once got to go 'behind the scenes' at Pietermaritzburg's Natural History Museum. All I remember is seeing a (dead and decomposing and very smelly) crocodile in a huge bath being prepared for, well, I'm not sure what, but some museum collection. That's when I first realized that there is more to a museum than just the exhibits. And since then I have been fascinated with what happens behind museum doors.
So, it's been great attending a course at Stockholm's Natural History Museum. Not only did we walk through exhibits on our way to work every morning, but we also had the opportunity to see where the museum personnel work and store their materials. Yesterday we climbed to the roof of the museum - which was fun and a little frightening (I seem to be developing a fear of heights as I grow older!). On our way up we passed the dusty and almost-forgotten collecting materials, still marked, of René Malaise, who was a well-known Swedish entomologist and explorer. Today we walked through the 3million-specimen insect collection and saw, amongst others, type specimens collected by Linnaeus' students. For someody like me, coming from a country with a relatively young history of science, this is exiting stuff!

databasing

What I like about this Bioinformatics workshop is that, after all the presentations we heard and the information we have been presented with, we have time to implement what we have learnt. We have three days to work on our projects. The advantage of this is that there is more opportunity to get a grip on the content of the course, and there is opportunity to ask people in the know-how for advice. I know for a fact that, had we not been presented this opportunity, I would have gone home and only gotten round to this work in a few months' time, and, of course, forgotten much! So, at the moment I am learning to use mySQL (another language... sigh). ;) I hope to make good progress on setting up my Fabaceae database before returning to Århus on Friday.

uBio

I have been perusing the many websites we have been introduced to. Lots of information and tools are available on these websites, so here I summarize the functions available on uBio (links to all tools provided on the website).

• uBioRSS- RSS feeds can be searched based on taxonomic names, as defined in the Species 2000 and ITIS Catalogue of Life 2007 Annual Checklist
• TaxaToy - plots the number of species discovered over time. This can also be queried according to taxon.
• OntoSpecies - provides links to browse taxonomic trees and provides links to several outside web resources
• LigerCat - Literature and Genomics Resource Catalogue
  
• Aging Portal -resource providing information on the lifespan and aging of species
• LinkIt - allows the user to retrieve taxonomic names (if I remember correctly, even ones that have been misspelled) from websites. (Apparently this tool is meant to be extended extracting info from pdfs in the future.) If these names are present in one of a number of other reference websites (e.g. nomenclatural websites, GBIF, phylogenetic websites, MorphBank, etc.), a link to these names on these other websites is provided.
• FindIT - taxonomic names are extraced from websites, free text or files that are uplaided (including pdfs). This is great if you want a list of species mentioned in a file/document.
• ParseIT - separates scientific names into their various components. Can be used for outputting in XML format.
• MapIT - All names in a document or website are extracted and... Well, the rest I don't really get. Will try to figure it out.
  
• CrawlIT - Crwals through a website and all links on that website and returns all the names mentioned there.
• X:ID - allows users to create their own identification keys which can be run over the web or locally.
  

XML Markups

Monday's session of the Bioinformatics workshop I have been attending and blogging about in the last days was the final formal session of the workshop. Donat Agosti, who heads up Plazi, entitled his talk "Literature & XML: or How to Have More Time to Think".
Before he launched into his presentation, Donat challenged us on our motivations for doing science and the reasons we get funded to do science at all. Regarding the last point, science is usually funded for advancements to be made in our knowledge of the world around us and for humanity. However, if this knowledge is unavailable to the rest of the scientific (or non-scientific, for that matter) world, science is failing what it initially really set out to do. So, Donat made a strong point for making science generally accessible and making use of non-copyrighted resources.
Donat then went on to explain how the information that is available in the written format (e.g. in papers) can be marked up using e.g. XML, and the information in these papers thereby made accessible in an electronic format. So, for example, if you publish about a species, info on its location, its host and a predator may perhaps be included in the manuscript. The words in the paper that describe the location, host and predator of the species could thus be defined as such, and accordingly link a species to a location, host and predator. Imagine a world where this information would be electronically accessible (and prevent us from browsing through paper after paper to look for what we need). I imagine that, in addition to saving us hours of time, it would open the door to a myriad of new ideas and analyses and provide a whole new level of understanding of 'how the world works'.
The major factor preventing large-scale marking up of published information is copyrighting. Only older papers can be marked up without violating copyright information. Currently, the Biodiversity Heritage Library (BHL) is scanning and marking up (for taxon only though) large quantities of old publications. When you visit the website, you can therefore search for a taxon and the scanned publications with page numbers (that are linked) can be accessed. If, e.g. your taxon's info is on pp. 98 of 329 pages in a publication, there is no need to trawl through pages of information to try find your taxon - you can go straight to pp. 98 where the taxon is mentioned.
Donat, together with Guido Sautter, a programmer, then went on to explain how they use GoldenGate Editor to mark up documents to XML. The process they use is somewhat slower than the BHL because it is more thorough. Instead of only marking up taxon names, they mark up other information such as taxonomic treatments, morphology, synonyms, etc. A great deal of the process is automated, so that only little input is needed from people.
Finally, the information that's extracted from publications can be linked to websites such as Zoobank, GenBank, be fed to GBIF, etc. There are a vast varity of options.