A Nobel Pursuit

Splitting the atom, unlocking the secrets of radiation, or even leading a peaceful civil rights movement.

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I grew up knowing that these were the sorts of achievements that earn you a gold medal and an invitation to Sweden in mid-December. I have since learned that the annual ceremony held in honour of Alfred Nobel hasn’t always been awarded to the most deserving candidate, and that sometimes the winners simply stumbled upon a discovery that changed the world. This was not the case with the 2015 Nobel prize for Physiology and Medicine. Continue reading “A Nobel Pursuit”

Money Walks and Talks in Academia

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As junior academics spend longer in their career, sooner or later, they start to realize that money matters more than anything when it comes to dealing with University Administration. Some will have this formalized in their tenure track agreement, but others will more blindly wander into it as promotion looms, and ask they get involved in developing plans for new hires in their department. Being wiser to this reality earlier on in my career might have helped me make different decisions along the way, or at the very least temper my idealism with a more natural cynicism.

 

For many academics, money (even one’s salary) is a secondary thought to research and teaching.  But obviously, these professional activities require money for them to function and often require substantial amounts for them to be done to a high level. You would be forgiven for thinking that where this money comes from is irrelevant and that its what you do with the money that counts, not just getting it.

 

As part of the economic crash that befell Ireland (and pretty much everywhere) sometime around 2008, the government accelerated is cut-backs to the 3rd level education sector. The latest figures I have heard kicked around my institution is that the government provides directly only about half the amount of money that is required to educate our students. This is an enormous shortfall to make up and doubtless troubles the sleeping patterns of our Provost and his administration greatly. Among the various options to bolster the funds are the usual suspects of international students (though in reality, although their fees are high, the government don’t supplement their place with additional funds, so its not really all that high when the money hits the red line), wealthy donors and of course overheads on research grants.

 

Different countries and institutions administer overheads differently, but generally there is some mechanism by which the university gets a percentage of the grant into a separate account to the research project which they can do as they wish (sometimes with conditions).  In Ireland, these might as much as 30%, but equally could be 0%. These overheads might be split, with some going to the PI that won the grant, some going to support PhD scholarships and some going who knows where in the black hole. Deans like big grants, because they come with big overheads, and this is where the trouble starts.

 

During a meeting to discuss the possible recruitment of a new senior academic in quantitative ecology, I was rebuked for naively pointing out that the person in question would be somewhat immune the current economic as their infrastructure demands were modest.  If you do expensive research, the financial benefits to the institution are larger than if your research involves a few computers for example. Dig up the cricket pitch, knock down the Arts Block and install a particle accelerator and name it after someone wealthy*. This is why disciplines whose research is cheap, and individuals who have low costs, face an uphill battle in gaining attention and reward for their work.

 

Money begets more money too. As well as PIs in receipt of grants receiving a portion of the overheads (not always the case even within my institution), some are then given additional monies from our national funding agency (as is the case for SFI who will give anyone with an Advanced ERC grant moving to Ireland up to €1million to smooth the transition!), but they are also rewarded indirectly with staff appointments in their research area (I suspect mostly as an easy decision that doesn’t need much thought beyond “there’s gold in them there hills”).

 

For my part, the grants I have held to date have not provided overheads of any note and I have benefitted indirectly from the grant successes of others, with my students accessing scholarships, stipend awards and travel expenses (though some of these funds come from philanthropic donations too). The reasons these grants don’t come with overheads are that the funding agencies in question argue that the PhD student fees they pay are there to cover the bench fees and associated costs for the student.

 

The most frustrating part is that all the research and teaching outputs in the world don’t make up for inputs in the form of cold hard euros. A recent internal missive from our institutional Research Office berating us for slipping down the world rankings by a whole 7 places, seemed to forget that many of the members of the academic community who contributed to our top 100 placement through hard-fought teaching and excellent research papers, books and other outputs, did so on a shoestring budget with innovative vim and vigour, in the face of cutbacks to our research, teaching and personal incomes.

 

We should all celebrate with our colleagues when they get the big grants as we all benefit from their success, and we collectively need the money to make the academic world go around. Those who win these grants need to remember that not every can and will be able to land these treasured grants and that they themselves were to some lucky on the day. Those running our institutions** need to remember that the success of any activity will ultimately be valued on its outputs and not who won the most money, even, in the end, university rankings.

 

 

*though I was pleased to read that Trinity recently spurned this approach so as to not turn off the not-quite-so-loaded donors.

 

**Interestingly, our nearest neighbours out at UCD handled their rankings very well, with a balanced and measured message to the community.

 

author: Andrew Jackson, @yodacomplex

Image: Wikicommons

Back to School.

Welcome back everyone.

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As the dusts settles on a hectic first couple of weeks, we finally have a chance to welcome everyone back from the much needed summer break (for those who got one).

We started this week with the exciting news that an alumnus of TCD Zoology, Dr William (Bill) Campbell has been awarded the Nobel prize for physiology and medicine with Satoshi Omura “for their discoveries concerning a novel therapy against infections caused by roundworm parasites”. Dr Campbell joins Dr Ernest Walton and Samuel Beckett as graduates of Trinity College Dublin to win the award. Obviously, exciting news such as this deserves its own blog post, so watch this space.

Tuesday brought with it the first Nerd Club of the year, as our research and teaching staff got together to plan the year of workshops, talks and presentations to keep us ticking over until May. As each week will cover different topics of interest to our readers, we’ll endeavour to write short openness to summarise the results of our discussions.

The Michelmas term brings with it the commencement of undergraduate teaching, and we are delighted to welcome back our returning Senior Sophistors, as well as our new crop of Junior Sophs, fresh from their marine field ecology trip to Portaferry.

ZooSoc has hit the ground running for the 42nd session, with dozens of events planned for the coming months under the guidance of Fionn Ó Marcaigh and his dedicated committee. Keep an eye on their Facebook, and twitter for details.

For regular news updates form the department of Zoology, be sure to check out Zoobytes on Facebook.

If you would like to contribute to the EcoEvo Blog,  please send us an email at ecoevoblog[at]gmail.com

 

author: Dermott McMorrough, twitter: @derm_mcm, email: mcmorrd[at]tcd.ie

The Skeleton in the Closet

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After a few ups and downs, everything you always wanted to know about the effect of missing data on recovering topology using a Total Evidence approach is now available online (Open Access)!

This paper also treats many different questions that people might be interested in (Bayesian vs. ML; how to compare tree topologies; comparing entire distributions, not only their means and variance; and many more!) but I’ll leave it to you to discover it…

Back on track, more than one an a half CPU centuries of calculation ago, Natalie and myself wanted to build a Total Evidence tip-dated primates tree. The Total Evidence method is the method that allows you to combine both living and fossil species (or actually, read “both molecular and morphological data”) into the same phylogenies. The tip-dating method, is an additional method that uses the age of the tips rather than the age of the nodes for dating such a tree. But I’m not going to talk about that in this post.

At the start of the project, we were both confident about the idea behind it and that primates would be the ideal group for such work since they are so well studied. A study that I described in a former post also came out around the same time, encouraging us and comforting us in this project.

However, as you might guess, something went wrong, horribly wrong! For the Total Evidence method, we need molecular data for living species (check) morphological data for fossils species (check) and also for living species (che… No, wait)! After looking at the available data, we quickly found out that there was a crucial lack of living taxa with available morphological data (check our preprint to be submitted to Biology Letters putting the actual numbers on the problem). From that problem, rose the idea of actually testing how that would influence our analysis. And funnily enough, this problem become one of the two major parts of my PhD!

Running thorough (and loooooong) simulations, we assessed the impact of missing data on topology when using a Total Evidence method. We looked at three parameters where data would be missing:

  1. The first one, was obviously the one I introduced above: the number of living taxa with no available morphological data (at all!).
  2. The second one, was the amount of available data in the fossil record (because yes, fossils can be a bit patchy).
  3. And the third one, the overall amount of morphological characters.

 

We then compared the effect of different levels of available data for each parameter individually and and their combination on recovering the correct topology, using both Maximum Likelihood and Bayesian Inference. For the correct topology, we used the tree that had no missing data in our simulations. For each parameter combination, we measured the clades in common between the correct topology and the trees with missing data as well as the placement of wild-card taxa (typically fossils jumping everywhere).

Unsurprisingly, we found that the number of living taxa with no available morphological data was the most important parameter for recovering a good topology. In fact, once you go past 50% living taxa with no morphological data, the two other parameters have no effect at all, even if you have a perfect or a really bad fossil record or many or really few characters. This is kind of intuitive when you think about it because the only way to branch the fossils to living taxa is to use the morphological data. Therefore, if there are no morphological data for the living taxa, the fossils cannot branch with them regardless of the quality of the data. Therefore, in this paper, we argue that to improve our topologies in Total Evidence, we should visit more Natural History museums. And not only the exciting fossil collections but the well curated collections of living species as well!

All the code for this paper is available on GitHub.

Check out the latest presentation about both papers.

Paper 1: Guillerme & Cooper 2015 – Effects of missing data on topological inference using a Total Evidence approach – Molecular Phylogenetic and Evolution (doi:10.1016/j.ympev.2015.08.023).

Paper 2 (preprint):  Guillerme & Cooper 2015 – Assessment of cladistic data availability for living mammals – bioRxiv ().

 

Author: Thomas Guillerme, guillert[at]tcd.ie, @TGuillerme

Photo credit: Thomas Guillerme (AMNH collections)

Vote for us in the blog awards!

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Our blog has been shortlisted for Best Education & Science Blog at the Irish blog awards. Public votes will represent 30% of overall score for this round of judging. So please, vote here if you enjoyed reading our posts over the past year.

Author

EcoEvo@TCD

Photo credit

http://noma-cdn.s3.amazonaws.com/content/Vote_Riso.jpg

Microplastics: a macro-problem for remote islands in the South Atlantic?

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Dr Dannielle Green from the Biogeochemistry Research Group in Geography is about to return from an adventure in the South Atlantic where she was hunting for microplastics in some of the world’s most remote islands.

Plastic debris can be found in every country around the world and larger items like plastic bags and bottles can have obvious impacts, such as entanglement, ingestion and suffocation of seabirds, turtles and mammals. But even when plastic breaks down, it persists as small pieces called “microplastics” and in this form can still cause harm to a wide range of marine organisms who unwittingly eat it. Microplastics have been found in marine waters all over the globe but sampling has mostly focused on areas adjacent to large human populations, very little is known about concentrations in remote islands like Ascension Island and the Falkland islands. In collaboration with Dr David Blockley from the South Atlantic Environmental Research Institute (SAERI), Dr Dannielle Green from Trinity College Dublin, Ireland flew out to the South Atlantic to assess the situation.

Eerily desolate but beautiful Ascension island
Eerily desolate but beautiful Ascension island

Water samples were taken from a range of sites around Ascension Island and the Falklands and every site was found to contain microplastics. In fact, the concentrations found were surprisingly high.

Taking water samples in the only glass bottles available... Pimm's bottles!
Taking water samples in the only glass bottles available… Pimm’s bottles!

Dr Green presented her work to the Falkland islanders by giving a public lecture at the Chamber of Commerce which was well attended with a mixed audience including government officials, fishermen, the general public and the local television crew. She explained the potential issues of microplastic pollution and a thoughtful discussion about solutions later ensued with input from the audience.

Dannielle presenting her results at the Chamber of Commerce in Stanley.
Dannielle presenting her results at the Chamber of Commerce in Stanley.

Microplastics can absorb toxic substances from the water column. In this way, they can become like “pills” of concentrated toxic chemicals that could be consumed by creatures like worms, shellfish, fish and mammals and can be transferred through the food web.

Pollution of natural habitats by microplastics is a global problem that we are only just beginning to understand, but it is one that is expected to get worse as plastic production continues to rise. Dr Green’s research explores the wider effects of microplastics on marine ecosystems. Through this work, she hopes to provide scientifically sound recommendations that will feed into policy and help protect our ecosystems.

Author

Dannielle Green

Photo credits

https://www.indiegogo.com/projects/save-our-seas-from-the-microplastic-threat#/story and Dannielle Green

Advice for new Faculty

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Congratulations – you’ve got your first Faculty position and you’re about to start! So you know you have to put together new teaching modules, get some grants and write some kick-ass papers. But in the midst of the head-down craziness of a new position it’s important to keep your eye on the ball. How do you make sure that in two years time you’ve been doing the right things and can progress at your new institution?

1. Get hold of the promotion form for your new institution, start filling it in and update it every 3 months or so. Do the same with the annual appraisal form, hopefully it’s similar to the promotion form! That way you can start building your portfolio and you don’t forget achievements. It also keeps you focused on the activities that you will be evaluated on. Try to talk to people who have sat on the promotion and progression committees to find out if there are other things you need to be doing.

2. Make active decisions about what you want to do rather than getting given jobs. Suggest to your manager potential service roles that fit with your interests & skills. If you’re asked to do something you’d really like to do but you don’t have time for then say that. “I would really love to do that but I currently have these other service/admin roles that prevent me from taking it on – is there a way of making room in my workload for this new job?”

3. Network within your new institution, you never know who will be able to help you out. It’s often easier to ask someone how a new task is done rather than trying to do it yourself from scratch, find those invaluable people who know the ropes.

4. The first 2 years are really tough no matter how well you do so cut yourself some slack. Most of the best things about being an academic never make it onto the promotion or appraisal portfolio. Count the successes & moments of satisfaction: improvements in your teaching evaluations, seeing a student get a concept due to your explanation, getting the funding to do something you are really passionate about, getting a paper published that you’re super-proud of. Don’t dwell on the missed deadlines (there will be many), rejections (there will be many, many) and frustrations (manyn) along the road.

And if you haven’t yet got that ideal academic position we’re hiring a spatial ecology/environmental biology permanent, fully funded, Assistant Professor at Trinity College Dublin J https://www.tcd.ie/Zoology/vacanciesindex.php closing on 18 September 2015.

Author

Yvonne Buckley

Photo credit

http://www.weenotions.co.uk/user/products/hinew.jpg

Summer in the city

summer-cityThe blog is going to take a well earned summer holiday and will start back again in September when hopefully we’ll have a slew of papers and conferences to report on! See you all soon.

Author

Adam Kane, kanead[at]tcd.ie

Photo credit

https://musiccourt.files.wordpress.com/2012/06/summer-city.jpg