Resources and Literature

The start of the new year sees me starting some new online training. I have signed up for

Microsoft: DAT204x Introduction to R for Data Science.

This is being run in conjunction with Data camp and since I have audited some of the content that they offer for free I thought I would give it a try. There is an option to pay for the course and get a certificate, I’m going to give it a go and see what happens.

I am currently in the midst of writing a paper and have had some interesting comments from co-authors about the age of some of the literature that I have quoted. I believe that there can be value in referring to literature that has stood the test of time, especially when it it is still being very widely quoted. I also think that using some “classic” literature with new literature can be an indication that the authors know the literature well since many search engines are set to display the newest first by default and so may not throw up those older references. I was pleased therefore to read this blog by Manu Saunders on Ecology is not a dirty word   which extols the virtues of older literature. Whether I am bold enough to send this to my co-authors, well that’s another blog topic altogether.

I received an email today from the team at the FSC Tombio project and amongst their new year news was this link to a neat little key to the major groups of British grasses  http://tinyurl.com/zymmadh . Written by Rich Burkmar it only tells you which groups your specimen is mostly likely to be from but it is free and very simple to use and does give an excellent starting point in the identification of tricky grasses.

 

 

 

Old dogs and new tricks.

As I mentioned in my previous post a trip to the NBN (national biodiversity network, @NBNTrust)  conference at York stiffened my resolve to be a more active biological recorder and caused me to get my kids out to Treswell, this month I have taken that a step further.

I have been a member of the tomorrows biodiversity project (@FSCTomBio) for a year or so without really getting involved, I read the tweets and looked at the courses, thinking that it was all a good idea and that one day I should attend some of their training. Well I finally signed up for their introduction to biological recording at Preston Montford Field Centre (@PrestonMontford). The course could easily have been dull, two people doing almost all of the teaching over long days (we’ve all been subjected to death by powerpoint right), but this was not the case. The course tutors, Charlie Bell and Rich Burkmar, worked really well together and bounced off of each other keeping things light and informal. I found the pitch and pace to be pretty good too, but the best part for me was the short session on earthworm identification which led to us generating data to record on ispot (@ispotnature).

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Students on the Introduction to biological recording course get stuck into earthworm recognition.

Talking to other students on the course I was interested just how many of them who were graduates or current undergraduates and involved in ecology felt that they lacked sufficient field ecology skills. This is a situation that resonates with me personally and I was very surprised at just how little attention was paid to this during my BSc in Conservation Biology, a weakness that I am now trying to address with external training. These points were brought even more sharply into focus recently when I read a blog post from BSG Ecology (@BSGEcology) explaining exactly what practioners are looking for in someone who is new to consultancy (http://www.bsg-ecology.com/what-are-we-looking-for-in-a-graduate-ecologist/).

To complete the new experiences I have taken tentative steps onto my first ever MOOC (massive open online course) this week having signed up for the future learn climate change course delivered in conjunction with Exeter University (@ClimateExeter). This is reckoned to take around 3 hrs a week for 8 weeks and participants are encouraged to blog about it so I will let you know how it goes!

A quick round up

Well November seems to have flown by! I’ve spent most of this month sitting in front of a computer wrestling with large data sets while trying to extend my knowledge and skills in R use.  I was, therefore, pleased when I got the chance to spend a morning looking around a couple of Lincolnshire Wildlife Trust’s sites. In the company of one of my supervisors and another researcher from Lincoln I went to look at the newly acquired Woodhall Spa airfield site. We were met by the knowledgeable and extremely enthusiastic Mark Schofield ( mschofield@lincstrust.co.uk) who introduced us to other colleagues on site. Mark told us that the trust had recently bought the site which was once the home of 617 Sqn RAF and that they had a raft of plans to restore it to its former glory. Thanks to the penchant for record keeping that exist among the British the trust has some amateur naturalists notes that describe how the site looked and what the species assemblages may have been at the end of the 19th century. Sadly the site has been quarried since the ’70s and it seems that insufficient thought may have gone into remediation when these operations began, as a result the soil types may have been mixed and soil chemistry is uncertain, this will make restoration a greater challenge. Despite this the trust have big plans for the site which could see it return to its former priority habitat status. I for one think that the trust deserve enormous credit for the vision that they have shown in taking the whole site in one go! I wish them well with it and hope that I might be able to get involved with a bit of plant species monitoring as the project evolves.

On the subject of our historic obsession with writing things down I followed my trip to Woodhall Spa with two days at the NBN conference held at FERA in York. This was a new thing for me, but I was pleased to be treated to a couple of days of interesting and informative talks from data gatherers and record keepers of all types. I was truly impressed by the recording skills of some of the junior recorders who have shown real dedication in the amount of records that they have logged in their short careers, this made me think that I should do something to facilitate my own children in making a start as recorders, a pledge which I kept when I took them to Treswell woods last week to have a go at identifying and recording some fungi. Ont the subject of Treswell the highlight of the NBN conference for me was listening to the indomitable Chris Du Feu regaling the audience with his tales of tree slug recording in the aforementioned wood and how he had managed to get this subject 7.5 minutes of R4 airtime, reducing the PM to 1.5 minutes into the bargain!

It was with a heavy heart that I read the details of the deliberate poisoning of the Masai Mara’s marsh pride of lions (made famous by big cat diary and other TV documentaries). According to National Geographic the local herdsman regularly graze cattle in the reserve under cover of darkness and the poisoning was a revenge attack after some cattle were killed by lions. Intuitively one would think that the Mara in general and these famous animals in particular would be a source of such revenue to Kenya that there would be a big incentive for local people to protect the wildlife but questions are (again) being asked about how much of this revenue trickles down to the local people.

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Male Lion (Google images)

Perhaps the biggest problem with this type of crime is that it is completely indiscriminate; so vultures and other scavengers are also affected. The poisoning of lions is worrying given that it comes against the backdrop of a recent paper by Bauer et al. which makes the assertion that, African lions, already listed as critically endangered in West Africa, are in such decline that in Eastern and Central parts that they ” may no longer be a flagship species of the once vast natural ecosystems across the rest of the continent”. Worrying indeed!

Back in harness with some book reviews

It has been a while since I last put pen (so to speak) to paper and produced a blog post. I got caught up in writing up my MSc by research thesis and then took some time away from university to gather my thoughts and prepare myself for the forthcoming PhD (now started in earnest). While I’ve been away I have kept myself busy (either earning money or overland travelling with my family in our classic Land Rover) but it is amazing how quickly one gets out of practice when it comes to studying, and how tiring it is when you return to reading!

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The revised version

My current project is largely computational and I have had to re acquaint myself with R, it is shocking just how much gets pushed to the back of the mind over the course of a year and it was an eye opening experience to sit in front of a PC and think “I am sure that I know how to do multiple regression in R, if only I could remember where to start!” I am pleased to say that a few hours with a trusted text has brought all of this back to me and I am now pushing ahead and learning new techniques.

The testats1xt that I have found most helpful in getting back to using R has been Mark Gardeners “Statistics for Ecologists Using R and Excel” . This excellent little book leads the reader nicely through the basics. Starting with how to down load R and getting data into the programme through exploratory statistics and into basic analysis with a section on reporting results which includes visualising data. It also makes it easy for the reader to synthesise R and Excel and there is extra help and sample data available on the free companion webpage if needed.  I recommended this text to the university library as well as to colleagues at my student workshops on R. Although I  initially bought this book when I wanted to discover R I actually also learned new techniques for data manipulation and management in Excel. I am given to understand that this book is being revised by Gardener  and look forward to seeing the new version.
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My new project will include some community ecology and a good deal of spatial analysis. I was looking around for a decent GIS text when a colleague pointed me in the direction of Brunsdon and Comber’s “An introduction to R for spatial analysis and mapping” . As a GIS novice I have found this book really useful although the data in the examples may be less overtly biological. I really like the way that the authors do not assume that the re reader is an expert in R but show where basic tuition is freely available rather than filling the book with very basic techniques. The book tells the GIS student at which level in R they need to be to start and this allows it to lead more or less  straight into the spatial content, it then combines this with more advanced R use such as writing functions and programming. Again data is provided via the companion website and the book is packed full of illustrations and code snippets, many of which have been added to my personal library for future use!

The final text that I have been using recently is another offering from Mark Gardener in the form of “Community Ecology, analytical methods using R and Excel”. In the interest of openness I should tell you that the publisher sent me a copy of this book and asked me to review it. This is a fairly substantial work from Gardener at well over 500 pages and the publishers say that it is aimed at advanced undergrads and post grads/ researchers beginning in community ecology. Without a doubt there is a challenge here since Gardener seekComm-Ecol-Covers to enlighten the reader about both community ecology as a topic (although he admits in the foreword that this is not exhaustive) and the analytical techniques needed to successfully study it. This is a feat which I felt that he managed reasonably well. I find his style easy going and he does well at not assuming the reader has expert knowledge. The book follows a logical path and is packed with reassuring screen shots and coding advice. The fact that it is written by an ecologist makes the data relevant to biologists and it all seems easy to follow, specimen data are again provided on the website. Gardener offers alternative analyses for each type of data, explains clearly when he thinks a particular analysis is most useful and then encourages the reader to ‘have a go’. I do have a couple of small criticisms though, firstly the book starts with a very basic introduction and I felt that it would better to point the reader to another source for this and secondly I have personally found that since using R for analysis my use of Excel has been limited to storing, manipulating and basic visualisation of data. With this in mind I found that the explanations of how to use Excel and then R, for the same analysis, were superfluous and that I skipped past the Excel parts to find how to do it with R. That being said, I guess that it is better to have too much information than not enough! Overall I found Community Ecology to be well written, useful and informative, and, as with the other volumes here I would recommend seeking it out.

A look back at the fellowship.

UFS 13/14 at the careers conference

UFS 13/14 at the careers conference

So February 10th, the date of the BES undergraduate careers conference, came and went. The conference was well attended and went pretty well, even if I do say it myself! The plan was to try and have speakers that the delegates could relate to, or who were in positions that the delegates could aspire to. I think that we achieved this in the main and we added in a couple of “big hitters” just for good measure.

Prof Bill Sutherland did the morning plenary slot for us and was as inspirational as ever! Telling the audience that although times may be hard there will always be a need for new blood in ecology and that those who are able sell themselves well will find a place. Prof Dave Raffaelli from York was next and talked about the science / policy interface and also had a few specific tips for the mature students in the audience. Robin Bisson from the science media centre was next followed by Jonathan Green from Liverpool who talked about academic careers; Jonathan had some particularly interesting points to make on the work /life balance.

networking 2 NetworkingUndergraduate conference delegates and UFS members network over coffee.

Coffee was followed by talks on the voluntary sector and ecological consultancy and the morning wrapped up with a panel session featuring the morning speakers. The afternoon session kicked off with a plenary offering from Julia Clause from the University of Rouen and INNGE. Julia was very charming and enthralled the audience while telling them how reflection is her major strategy when it comes to managing her “modern ecological career”. Julia was followed by Ross Mounce from Bath who spoke about using social media to manage an ecological career and raise your profile. This was the second time I had seen this particular offering from Ross but he is always good value and there is always something to gain from his talks.

A round of short talks from Sarah Blackford (can you have a Life Sci careers event without Sarah’s name coming up?), Dominic Andradi Brown, Myself and Julia (who spoke about INNGE this time) was followed by fun networking session and a final panel session. Then it was time to wind down with afternoon speakers making themselves available for an informal chat over a glass of wine.

I would like to personally thank Katherine Maltby for all of the help and support that she gave us. I also want to thank the other Fellows for the effort that went into the conference. Inevitably some of our number were away on research trips or had gained jobs and were keeping the wolf from the door, whilst poor Katie was having a knee op! and so not everyone made it to the event, but they still helped massively with the planning and tweeted their support from various locations on the day.

UFS 13/14 at INTECOL

UFS 13/14 at INTECOL

The careers conference is the final event in the fellowship calendar and we are left to look back on a pretty cool year while Karen and Katherine appoint the lucky undergraduates who will replace us. The fellowship is not about being spoon fed with opportunities but does give you a pretty good insight into the world of the BES. It lets you meet some fairly senior people you might otherwise find it difficult to meet, gives you experience of how the Society operates but most of all introduces you to a bunch of other like-minded individuals (including the fellowship alumni) with whom to go on a journey. Would I do it again?  YOU BET!

Thinking about output and health and safety.

As an early career ecologist I seem to spend a bit of time generally ruminating and mulling over ideas whilst making decisions and choices. Recently I have been thinking about the output that my current project might generate and . having recently developed an interest in citizen science I think that if we are to use data collected by the masses then we should at least make the output that is generated accessible to any interested party who had a hand in generating the data. This means writing in a manner that is intelligible and interesting (see Sand-Jensen’s  How to write consistently boring scientific literature)  but also publishing somewhere that people can access the stuff! So one of the things I have recently been pondering is whether to try and persuade more senior co-authors that we should publish work in open access journals such as f1000 research which is publishing ecology papers free of charge until the end of this year. The whole open access debate has been focused to some degree by the recent ‘who is afraid of peer review article in Science Magazine. Responses to this article seem to range from quiet approval from those happy with the print journal system to this blog post by Jeroen Bosman with Bob O’Hara writing what seems to be a moderate and well thought out response in the Guardian. You don’t need to be Einstein to look at the author pays model to work out that it is readily open to abuse and that  junior scientists who are keen to get work published and are perhaps more naive are susceptible to being targeted.

I wrote in a recent blog post about Hoffmann discovering the effects of LSD by taking some and then going on a bicycle ride. Thinking of this while considering COSHH, risk assessments and ethics forms for my current project my attention was drawn to Micheal Mosley’s current BBC 4 series Pain Pus and Poison. With no mention of health and safety, Mosley details how, in 1815 Friedrich Serturner had isolated some crystals which he and his  lab group tried in different doses to see what effect they might have. It is staggering enough when you realise that the crystals  that they were gaily knocking back were morphine but Mosley goes on to detail how  Serturner and his colleagues were dissolving these opiates in alcohol to aid ingestion! Now there is a risk assessment I would like to read!

As conference season draws to a close I had the good fortune to attend my first BES special interest group meeting. This was organised jointly between the computational ecology group and the International Biometric Society and it looked at species distribution modelling, my thanks go to all who were involved in organising this informative event.

Rock pooling with Yorks branch Society of Biology

My trip to London followed hot on the heels of a weekend visit to the N. Yorks coast for, among other things, a  day of rock pooling at Boggle Hole with the Yorks branch of the Society of Biology. Thanks go to Clive Tiney and others for organising this and to all of those who attended with more knowledge than Henry and I and who helped to make this an enjoyable day by selflessly sharing their time and knowledge. Henry (aged 8) has decided that he wants to be a marine ecologist because “crabs are really cool”

I’d like to finish by mentioning a funded studentship at Lincoln with Anna Wilkinson on social cognition and reminding the students out there that you can get a years free membership of the BES here this applies to undergrad / masters level and again for PHD.

Making sense of all that science or maybe not?

With INTECOL firmly behind me (phew) and my research project stretching out in front of me I found myself sitting at my desk today wondering what my next blog post should contain.

I was thinking that perhaps I should revisit some of the notes that I took at conference and write a second INTECOL post when a blog about taking the most from conferences arrived in my inbox. Now, while this advice may be a bit late for me this year, it did make me think. The main plank of the advice proffered seems to be that the social aspect of conference (networking and team building rather than just drinking for its own sake!) is by far the most important. It is true enough that anyone wishing to get more detail on the science presented at a conference need only Google the author and get a PDF from the horses mouth.So perhaps my time was well spent on those late nights after all!

As a junior scientist at the end of my first conference season it is not really the detailed science which is vexing me, I have an altogether bigger problem! I started the summer with interests in a couple of different areas and hoping that I would narrow this down and find a subject to specialise in but I have been exposed to so many interesting people that I now have broader interests! Just how do you choose, or perhaps you wait to be chosen!

Finally my kids went through the stuff I bought back from London and Henry (age 8) saw the INNGE badge and asked what it stood for. When I told him he said “did you bring that for me because I am the next generation of ecologists?”  “Of course” I replied. He is already working on his French for 2017!

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