EcoEvo@TCD, Author at EcoEvo@TCD

19/04/201305/04/2019

School of Natural Sciences Postgraduate Symposium: Part 1/4

Postgraduate students from Trinity College Dublin's School of Natural Sciences — Postgraduate students from Trinity College Dublin’s School of Natural Sciences

On the 15^th and 16^th April we had one of my favourite events at Trinity College Dublin: the annual School of Natural Sciences Postgraduate Symposium. Over the course of two days many of our PhD students presented their work to the School. We also had two amazing plenary talks from Dr Nick Isaac (CEH) and Professor Jennifer McElwain (UCD). For those of you who are interested in exactly what we work on here at EcoEvo@TCD, here are the abstracts from the PhD student presentations. Check out the TCD website for more details! Continue reading “School of Natural Sciences Postgraduate Symposium: Part 1/4”

17/04/201318/04/2013

Hide and seek with a T-Rex in a drawer

Natalie Cooper and Sive Finlay already posted on this blog about the amazing old stuff you can find in a Natural History Museum (here and here). Palaeo collections are also special, I spent one week in the Smithsonian Institution Paleobiology collections to measure some Eocene American primate teeth and I was amazed by the quality of their collections. But the nice thing about Palaeo collections is that when you’re looking for a particular specimen, you always come across wonders you didn’t expect.

USNM-299811 — …Each one containing tiny fossils, like this *Tinimomys* molar.

…With some weird Helicoprion spiral teeth!

Oh and yes, not to mention the dinosaurs such as this hadrosaurid skull…

And I even found, hiding in a drawer… a T-Rex!

Author

Thomas Guillerme: guillert[at]tcd.ie

Photo credit

Thomas Guillerme, with the kind permision of Michael K. Brett-Surman.

15/04/2013

Disney Ecology

In light of the current stresses of exam season, I have been contemplating my parallel educational history. Of equal, if not superior, importance to any stage of my conventional academic life, I have had a Disney education. If I visit medieval castles or forts rich in feudal history I can’t help but mentally locate Rapunzel’s tower and contemplate the prince’s access route. My Greek mythological references are entirely based upon Disney’s Hercules and any mention of Rudyard Kipling is incomplete without at least one verse of the Bare Necessities. Zoological education is no exception. Early Disney films were rather loosely based on real zoological principles – I don’t remember Snow White using any Pavlovian theory to behaviourally condition her furry friends to help with the housework. Similarly, Mary Poppins serenaded an American robin from her London home because studio executives thought the sight of a European robin would be too confusing for their target audience. However, some recent Disney tomes are more grounded in realistic ecology. Disney was my first introduction to fundamental ecological and behavioural concepts as varied as breeding coalitions, mutualistic relationships and inter-specific communication.

Responsible for introducing Swahili phrases to a generation of Timon and Pumbaa fans, the Lion King is a Disney classic, both as a film and more recently as a highly popular stage musical (which is coming to Dublin soon – even if you don’t normally like musicals you must go to this show for the most incredible stagecraft you will ever see). The film marked one of the first times that animators made a specific effort to study their animal subjects to make their movements and behaviours as realistic as possible. Prior to the release of this film, my four-year old self didn’t know that male lions, often brothers, form coalitions to take over prides or that female lions take a cooperative, crèche approach to raising their offspring. Cooperative behaviour in lions continues to spark interest and research to understand why lions are unique among big cats in exhibiting these social tendencies. Of course, some creative licence remained in Disney’s depiction of their feline heroes – the voice of Darth Vader is sadly absent from the Serengeti and male lions don’t lead a troupe of goose-stepping hyenas in a song of revolution. Similarly, rather than a “king and queen”, there’s an equal dominance status within male members of a coalition and within adult females in a pride (unfortunately socially equal characters don’t lend themselves easily to a re-telling of Hamlet). Despite the sprinkle of Disney magic however, the basic ecological premise of Simba’s pride remains grounded in fact.

My ecological horizons were further expanded by Finding Nemo’s depiction of the mutualistic relationship between clownfish and the anemones they call home. It’s a deceptively simple relationship – the anemone’s sting provides the fish with a predator-free habitat while Nemo and his friends help keep the anemone free from parasites. However, many of the finer details underlying this interaction continue to spark research interest (and I’m obviously not the only one to have experienced a parallel Disney education). Nemo has provided evidence that mutualistic interactions tend towards a nested structure. More recently, the way clownfish move their fins has been identified as helping to increase anemones’ oxygen consumption at night – although, hampered by a malformed fin, I wonder whether Nemo’s personal anemone is gasping for breath a bit more than the other anemones? Furthermore, Finding Nemo did not neglect my geographical education – I now know that to get from the Great Barrier Reef to Sydney it’s just a short ride on the East Australia Current – and if I meet a turtle on the way, just call him “Dude”, Mr Dude is his father.

Thanks to Disney, Nemo’s pal Dory is another star of every aquarium. Forgetful but lovable, Dory was my first introduction to the realms of interspecific communication. While Dory speaks whale, it appears that some whales can learn to talk back. A captive beluga whale in San Diego seems to modify its call to mimic human speech. Neither of these examples are true interspecific communication; Dory’s valiant efforts to converse were unsuccessful and the Californian beluga’s “human” vocalisations appear to be relicts of an ability to mimic other whale species. In both cases, information is not passing between fish and whale or whale and human. Though who knows, perhaps Finding Nemo 3 will be a story of the quest to discover the Rosetta Stone for interpreting whale speech…

So through the talking animals, improbable alliances (why a meerkat and warthog??) and heart-warming moral tales, look out for the ecology in your next Disney film. Combining their subliminal ecological messages with the excellent work of the Disney conservation fund hopefully many more generations will experience a Disney ecological education.

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credit

wikimedia commons

12/04/2013

Finding a PhD

Undergraduate and Masters students often come to me for advice about how to find a PhD position. I know quite a few students read this blog so I thought I’d share the advice here. Hopefully some of it is helpful! Note this is aimed at people in the UK and Irish system who often go straight from undergraduate to a PhD (or do a brief one year Masters course in between the two). But many points are relevant to the US system too.

1) First make sure you definitely want to do a PhD!

This is really important and I think it’s something that very few of us ever bother to do. The thesis whisperer has some amazing advice on this, and many other subjects related to PhDs, so I won’t repeat too much here. (See http://thesiswhisperer.com/2011/11/07/should-i-do-a-phd/)

Doing a PhD can be an amazing experience, but it can also be extremely frustrating. Often it’s amazing and frustrating at the same time! You will work long hours for several years with very few rewards and low pay. Then once you finish your PhD things get even trickier – there’s no job security until you reach the Lecturer/Assistant Professor level which generally won’t happen until you’re at least 30, and getting that lecturer’s job is extremely difficult as there are far more qualified PhD students than there are postdoc jobs and lecturer jobs. So to succeed you need to work really hard and also have good luck. It’s good to aim high, but it’s also worth having an alternative career plan in mind for if the whole academia thing falls through. So before you start the long road of potential academic misery, make sure you have a really clear reason WHY you want to do a PhD. If it’s because you love research and can’t imagine doing anything else then great! If it’s because you need one for your chosen career (within or outside academia), again great! But if it’s because you don’t really know what else to do after graduating, or because you want to be a student for a few more years, then I’d recommend researching other options.

2) Advertised PhDs.
These PhDs generally already have funding and a planned research project. You just need to apply. Applications are usually fairly simple, just a CV and cover letter plus a couple of references (usually two). For the cover letter, make sure you describe exactly how you meet the criteria in the job description. Check out our earlier blog posts for help with CV writing. For referees try to include academic referees. Your project supervisor would be a good person to ask, followed by the head of department or your tutor. If the position is in aquatic ecology and you did particularly well in your aquatic ecology module you could ask the lecturer who taught you. Make sure you ask people before you put them down as references.

PhDs are advertised in many places including:

Twitter (with #phd or #jobs)
www.findaphd.com
ECOLOG Archives
Evoldir
University websites

Twitter can be particularly useful for this, as lecturers often tweet about positions in their lab and retweet adverts from other lecturers.

3) Non-advertised PhDs.

Not all PhD positions are advertised. Sometimes this is just because the person taking on students already has someone in mind or a good pool of undergraduate students to choose from. More often though this is because although the lecturer is perfectly happy to have a new PhD student they don’t have any funding. In these circumstances you need to apply for your own funding.

There are a couple of options when it comes to funding. The simplest are “personal” awards or studentships. These are PhD scholarships given to individual students based on various criteria – usually the quality of the student and of the proposed project. The other option is that a supervisor may include PhD student funding on a larger grant they are applying for. In this case the responsibility for the application rests with the supervisor. For personal awards the responsibility rests with you.

To apply for your own funding you first need to find a possible supervisor. You should already have an idea of the kind of project you’d like to work on, so you can use the internet to search for supervisors who might fit your interests. Ask around your current lecturers to see if they know of anyone suitable. You can narrow the search by also thinking about the place you’d like to study at. Once you’ve identified a possible supervisor, send them a brief email with your qualifications (attach your CV), what you’d like to work on, why you’d like to work with them and ask if there would be any opportunities in their group. Also mention that you’d be happy to apply for funding (if you have a funding body in mind mention this too). Don’t do this as a bulk email; make sure it’s tailored to the person in question. Also make sure it’s brief; most people today read emails on mobile phones so long emails are annoying.

If they say yes then you can work with them to prepare a proposal. Don’t get discouraged if you don’t get replies or if you get lots of negative replies. It’s not personal, it’s just that people are busy and some already have as many PhD students as they can handle!

One quick tip on choosing a supervisor (again thesiswhisperer has lots of advice for this): don’t just focus on the senior people. It’s exciting to work with a famous scientist, but more often than not they are extremely busy and their groups are hard to get into. More junior people are often given money for a PhD student or two when they start a new job. They also tend to have more time.

4) Where to apply for funding.

The best thing to do is to talk to your potential supervisor about funding options. There are fewer and fewer options these days but each university usually has some kind of scheme, and scholarly societies often give out scholarships. What you are eligible for will depend on the project, your nationality and the country you wish to do your PhD in. For example, EU citizens can get funding from Marie Curie/European Commission if you do a PhD outside of your home country (and in the EU). Students of any nationality can apply for funding from the Irish Research Council to do a PhD in Ireland. Students of any nationality can also apply for a Trinity Postgraduate Scholarship or Ussher Scholarship from Trinity College Dublin if they wish to study at TCD.

5) DO NOT accept a PhD with little or no funding.

Some people are so keen to do a PhD they’ll accept one with little or no funding. This is a terrible idea (unless you’re independently wealthy!). You will need to pay fees (at TCD these are currently nearly €6000 a year) and need money to live on. Many people try to manage this with a part time job, but if you’re working you’re not doing your PhD, which should be a full time job in itself. And remember for every extra year doing your PhD you need to pay fees. This doesn’t even consider where the money for lab materials, conference travel or equipment is going to come from. So make sure you check the status of the funding before you say yes!

6) Qualifications needed for PhD positions.

If you only have an undergraduate degree then you need a 2.1 or 1^st class degree. Remember you’ll be competing with lots of people when you apply so this is just a guide. You can get a PhD with a 2.1 BUT if all the other applicants have 1^st class degrees you will struggle. I personally would prefer a student with a 1^st for their project and a 2.1 overall, to a student with a 2.1 for their project but a 1^st overall.

If you have a Masters then you may get a PhD with a grade lower than a 2.1 but only if you got a good grade on your Masters (preferably a Distinction). Again, your mark for the project component is the most important.

If your qualifications are unusual make sure you explain them. Also make sure you explain them if you are applying to a foreign university which may use a different system. Percentage marks often help here. If you know where you ranked in your class include this information too. If applying for positions in the UK, Irish students should highlight the fact that Irish degrees are 4 years long thus almost the equivalent of a degree and a Masters in in UK.

7) Should I do a Masters or work experience?

Masters courses can be great but they are also expensive and may be of limited benefit in some cases. If you don’t feel ready for a PhD, or are unsure you want to commit to a PhD, a Masters may be more sensible than jumping straight in to a PhD. Also if your grades in undergrad were not very impressive, doing a Masters and getting a Distinction or Merit can override these issues. However, if you’re certain you want a PhD and your project and overall grades were good at undergrad there’s no reason you shouldn’t apply for PhDs straight away. One solution might be to apply for Masters courses and then pull out if you get a PhD (check your contract so you don’t end up losing any money). Masters in Research (MRes) courses may be a particularly good idea as they involve several research projects so allow you to decide if you really like research or not. MSc courses also include taught elements, so these are good if you want to learn more about a specialised topic. These also end with a long research project.

If you want to get a field or conservation based PhD, then work experience may be a better option than doing a Masters. This may still be expensive as most of these positions are unpaid, but then you have the option of volunteering for some of the time and then working to support yourself. Work experience can be Research Assistant positions at universities, internships at conservation charities etc. The Institute of Zoology take interns every year, as do the IUCN. There are field projects on meerkats and baboons run out of Cambridge University that take volunteers each year. Also search ECOLOG and EvolDir (see links in 2 above) for other field assistant positions. Alternatively, if you have a potential supervisor in mind you could email them and offer your services. Or offer to help at a local university so you can live at home and save money. Research Assistant jobs are a great way to learn about PhDs and research from PhD students and researchers you interact with, however, you have to be prepared to work independently as people often don’t have much time to supervise interns.

That’s my advice! Feel free to add alternative advice if you have any. And good luck finding a PhD!

Author

Natalie Cooper

nhcooper123

ncooper[at]tcd.ie

Photo credit

PhD comics

10/04/2013

Icefish: The coolest fish on the planet

I love fish. Not (just) to eat, but to study and learn about and at times just marvel at their beauty. They are arguably the most diverse vertebrate group (and easily arguable if you take the cladistic view that all vertebrates are, at heart, just highly modified fish). But even focusing solely on actinopterygians (ray-finned fish) every aquatic niche is filled by one species or another, from the poles to the equator, from the high Tibetan plateau to the depths of the ocean where sunlight is a distant memory. If there’s water chances are there’s fish.

My particular passion is for deep-sea and polar fish. They have, in my opinion, some of the weirdest adaptations to their environment and I’ve reached a point (right around the time a fish with a transparent head was filmed in the wild!!) where nothing they can do can surprise me.

Despite my jaded outlook I like to keep an eye out for interesting news stories and the other day I stumbled across a story in the Independent about a ‘mysterious fish with clear blood’. I read the story with increasing disappointment as I realised the fish was mysterious only to the reporter, but it provides a perfect opportunity to share the wonders of icefish with a wider audience.

Icefish (Channichthyidae) live in the Southern Ocean. They are a family in the suborder Notothenioidei, a group found in the Antarctic and sub-Antarctic, and have been a love of mine for almost a decade. Notothenioids live in water which reaches sub-zero temperatures, but where their softer, lower-latitude relatives would freeze instantly, they swim merrily on. They can do this due to adaptations, one shared by most Notothenioids and one unique to icefish.

The first adaptation is, in every sense of the word, the coolest I know – they have evolved antifreeze! Antifreeze glycoproteins to be exact. These AFGPs inhibit the growth of ice crystals and prevent the blood and tissues from freezing.

The second adaptation, found only in icefish, has resulted from the interplay of two properties: at low temperatures fluids become viscous and large molecules, such as haemoglobin, increase this viscosity further still; and oxygen solubility increases as water temperature decreases. Icefish have exploited this second property to counter the first. Haemoglobin is an oxygen carrier, but at low temperatures it becomes more of a hindrance than a help. Icefish have a leathery skin instead of scales, allowing oxygen to be transported across their skin as well as their gills, and the high oxygen concentration in the water means that the haemoglobin can be lost with little reduction in oxygen capacity which is exactly what they have done. It helps that these fish aren’t exactly active, preferring to wait for prey to come their way than actively seek it out, but even so I think there are few other animals that could lose haemoglobin and still be alive, let alone live with few negative consequences.

The most striking consequence of this loss is that icefish have white flesh and gills. Normally gills are one of the reddest parts of a fish due to the need for blood to collect oxygen as water passes over them. But in icefish their gills are white; freakily so.

The news story, originally from AFP and posted almost verbatim on several websites, was extraordinarily hyperbolic. It gave the impression that haemoglobin- and scale-loss were unique to this species. Yet, as I’ve said, haemoglobin loss is found in all members of the icefish family and scale loss is found in many species.

The real story is that they have managed to get the species to spawn in captivity, which is a fantastic achievement as anyone who knows anything about closed life-cycle aquaculture will know. Unfortunately it seems that this legitimate success is not sufficiently newsworthy and so a false story has been created. The upside I get to talk about one of my favourite fish so I guess it’s not all bad news!

Author

Sarah Hearne: hearnes[at]tcd.ie

Photo credit

Sarah Hearne

08/04/201308/04/2013

Top tips for science networking!

Science is a business like any other, and it’s hard to get things done if you don’t know anyone outside of your own department. Other scientists will review your papers and grants, invite you to give talks and hopefully employ you in the future. So the more people you know, the easier it gets. Conference season is just around the corner so I thought I’d continue my hints and tips series by talking about networking at conferences.

Step 1: Finding someone to network with…

Find someone you know and get them to introduce you to everyone they know. This person may be your supervisor, but postdocs and other PhD students can be just as helpful. Make sure you return the favour then everyone will know plenty of people! If you know several people, spend time with each of them meeting all their friends and maximizing the number of new people you meet.

It’s pretty rare to go to conference where you don’t know anyone beforehand. This is much harder than option 1 because you constantly have to make the effort to talk to new people which is pretty exhausting. In these situations try asking your supervisor beforehand if they can remotely introduce you to at least one person there. Then follow them around until you make new friends!

Go to conferences with easily achievable networking goals, for example choose one big name in your field and make sure you have a conversation with them, even if it’s short. However, don’t be that person who goes to conferences with a list of “important” people they want to meet and spends the whole time pestering the big names and ignoring everyone else. The people with the time and energy to start exciting new collaborations are usually students or postdocs, and these are also the people you’ll be meeting at conferences for the rest of your career. So make sure you network with them too!

At huge conferences like ESA it’s often hard to casually network because everyone has already scheduled meetings for every lunch break and evening before they arrive. If you really want to meet with someone drop them an email beforehand and see if you can arrange a quick meeting. Make sure you’re really specific about the meeting place, and don’t be too upset if they don’t show up, they were probably intercepted on the way!

Use social media! Twitter is a great way to arrange tweetups at conferences, and some societies also have Facebook pages where events are advertised. I haven’t tried this yet but I’m very excited about trying it at Evolution and ESEB this year.

Go to all the drinks receptions you can, but skip the conference dinner. This is just my opinion, but I’ve never done any good networking at a conference dinner. They can be fun, but usually they are at the end of the conference so everyone is hanging out with their friends and not really in the mood to talk about work. They are also expensive and the food is often awful. I usually go for dinner with some friends instead and we usually meet other people who aren’t at the conference dinner so we get to make new friends that way!

Step 2: OK so I’m chatting to a new person, what do I say?

I think you should always aim to have a person walk away from a conversation knowing the following pieces of information: your name, your institution and roughly what you work on. Aim to do the same with everyone you meet. If you meet someone particularly relevant to your research interests make a note of this before you forget.

Before going to a conference make sure you have a series of “elevator pitches” prepared. These should be the 1, 5 and 10 minute versions of what you’re currently interested in or working on. If you’re looking for jobs you should also prepare a quick outline of what you’d like to do in the future and the ideal place you’d like to work.

Be interested and interesting. Being interested just involves asking the other person about their work. Everyone likes to talk about their current pet project, and in general these are interesting so you don’t have to fake it! Ask questions where appropriate and be enthusiastic even if you couldn’t care less. If appropriate refer back to their talk/poster or recent papers. Being interesting is harder but again being enthusiastic helps. Talk about your work or the talks you’ve enjoyed at the conference or current areas in science that fascinate you. Hopefully after a somewhat artificial start to a conversation you’ll find yourself in a real and enjoyable chat.

Provided you get in a tiny bit of information about what you’re working on, you don’t have to talk about your work the whole time. Feel free to bemoan peer review, or the funding crisis or the bizarre nature of your structured PhD program. These are great conversational topics as everyone has an opinion and they affect all scientists. Also don’t worry about talking about normal topics – family, hobbies etc. Even the big names have lives outside of academia.

Step 3: Damage control (or OMG I can’t believe I just said that…)

One or two beers are your friends! Alcohol is a great way to reduce inhibitions and help you to chat to people you’d be too terrified to approach when sober. Three or more beers (depending on your alcohol tolerance) are not your friends. If your inhibitions are reduced to the point of dancing on the table people may not remember what you work on. Though they will remember your name…

To be fair, conferences often do involve a lot of drinking and it’s naïve to think you can avoid this entirely. People come to conferences to see old friends and enjoy themselves as well as for work so this should be respected. I think the rule of thumb for alcohol at conferences is to try and hang around with people at the same level of inebriation. Don’t be the drunk group in the quiet bar surrounded by sober people. Also remember that you need to get up the next day and go to lots of talks, so being hungover is not a good idea. Know your limits and never feel pressured into drinking if you don’t want to.

Don’t worry about making a fool of yourself. I’m the champion of this and somehow I still got a job. My classics (all while completely sober) include (1) being put in charge of cake at a meeting in London Zoo and promptly falling over and throwing all the cakes on the floor in front of the director; (2) missing my mouth while talking to a big name at Evolution and pouring coffee all down myself; (3) accidentally wearing a dress you could see my underwear through when meeting the Duke of Edinburgh; (4) complaining that an eminent scientist who published a lot of similar papers would probably publish their shopping list if they could – then realizing the person I was talking to was the scientist’s co-author; (5) insisting that ducks weren’t birds in front of an ornithologist (there’s a logical reasoning behind this but they didn’t stay to hear it); (6) trying to tap someone on the shoulder and accidentally stroking them instead etc. Most of these incidents are not remembered by anyone but my colleagues, and I don’t think they have influenced my career. So if you do say or do something ridiculous, don’t let it scare you away from talking to people in the future!

Those are my top tips; I hope some of them are helpful! I should point out that I don’t actually follow most of them, but I do try my best! Feel free to add more tips in the comments!

Author

Natalie Cooper

nhcooper123

ncooper[at]tcd.ie

Photo credit

wikimedia commons

05/04/201305/04/2013

What makes a good undergraduate (or Masters) thesis?

Here’s something that few students realize, and even fewer believe: your lecturers and professors actually want you to do well! I gave this advice to the final year undergraduates in October, and now they’ve handed in I thought it might be valuable to share it more widely. Note that they are in no particular order and I’m not talking about specific projects.

1) Do not annoy the people marking your thesis.

Most of my advice comes back to this point! Remember that most people marking your thesis will be marking a lot in a very short time (although this varies among institutions and subjects). Therefore if you make this as easy for them as possible you’re more likely to get a good grade.

2) Read the marking scheme carefully.

For example, there’s no point in listing every single thing you did if there’s no effort mark. See point 3.

3) Be concise.

There are two reasons for this. Firstly, having to read a 10,000 words (or more) monster thesis is going to make your marker grumpy before they even open it, especially with 5-10 theses to mark each year. You won’t be marked down for that (though most places have penalties for going over the word count), but you may find the marker more likely to notice other problems (see point 1).

Secondly, and more importantly, a long thesis usually indicates a lack of understanding of the really interesting findings of your research. Almost anyone can collect data from the lab, field or the literature and then go away and analyse it in every way possible. However, it’s a real skill to pick out the key results and discard the extraneous information. All of the best theses I’ve seen have been short (though I’ve also seen some terrible short theses!). They have an introduction that concisely builds towards their aims/questions, clear predictions, methods and results describing succinctly what they did to answer their questions and whether their predictions were met, and then a careful discussion of how their results fit into the wider literature. Showing every single thing you did is NOT going to get you more marks (see point 2).

People have a horrible habit of writing too much in the introduction. Think very carefully about what the reader needs to know to understand your questions. If you’re working on tortoises in Ireland in field site X, does the reader need to know what a tortoise is? No. Do they need to know where Ireland is? Not really. Do they need to know where your study site (field X) is? Not really, unless you only want to apply your results to field X or if field X is really special or weird. They may need to know the species of tortoise or the climatic conditions at your site but that shouldn’t take more than a sentence.

4) Presentation is really important.

I sometimes joke that you can work out the class (1^st, 2.1, 2.2, 3) of a thesis just by looking at how it’s presented, particularly the reference section. However, there’s a lot a truth to this. If you take care on the presentation, it usually means other aspects will also be good. Part of this is a time management issue. I know it’s difficult but if you can complete your thesis a few weeks early you will have time to polish the presentation and probably to deal with other minor issues in the thesis. Note that many places give marks for presentation so even if you struggled with some aspects you can pick up a few extra marks just by fixing the typos and formatting your references correctly. Note that this is a great thing to do when your brain is too tired to do any more writing or analyses.

5) Take advantage of people who offer to read drafts.

Chatting about this at coffee the other day we estimated that students who got their supervisors to read a draft of their thesis before handing in got a mark that was around 5% higher than it would have been otherwise. 5% might not seem much in the grand scheme of things, but if you got 66%, 5% extra would get you a 1^st… Also take advantage of family and friends for their proof reading services. A great idea would be to do this early and often with your classmates, perhaps reading each other’s work section by section. Again this requires you to have good time management skills – if you want your supervisor to read something make sure you give them AT LEAST a week to read it and AT LEAST a week for you to deal with corrections.

6) Structure is really important.

When writing your thesis imagine you’re telling a story. You start with the background and general area of the study and slowly progress towards the specific questions you are going to address. You then explain your methods, continually referring back to how these methods will answer the questions you want to address. In your results, show how your analyses answered your questions. Finally in the discussion show how your results fit within the published literature and then talk more broadly about what they mean for the subject area. Your questions and aims need to be clear throughout so make sure they are linked together.

7) Be careful with subheadings.

I’m a big fan of subheadings but it’s very easy to overuse them and to use them so you don’t have to link sections together. Even with subheadings, there needs to be some kind of link or the sections become disjointed and your story gets lost. They are ideal for separating major themes in your thesis – for example I always advise my students to have subheadings in the methods section for DATA COLLECTION and ANALYSES.

8) Don’t worry if your final thesis doesn’t match your proposal.

Things change all the time during projects. Perhaps your experiments didn’t work so you had to change them, perhaps there wasn’t enough data for you to test your hypothesis, perhaps you couldn’t catch any of your chosen study animal. Of course these problems are frustrating but they shouldn’t affect your thesis (trust your supervisor, they will help you fix this!). However, when you come to write up make sure that your introduction matches the question you ended up asking, not the question you intended to ask. I know it’s painful to set aside all the work and reading you did for your proposal, but you won’t get credit for irrelevant information (see point 2).

9) Analyses in methods and results

Students often get confused in these sections. As a guideline, although you don’t need to understand the maths, you do need to understand WHY you are doing the analyses you are doing. Which of your questions are you testing? Why are you using a t test or an ANOVA? Why did you log your variables? In the results explain what the result means biologically – i.e. if you have a significant correlation between body size and shell size in your tortoises write this then give the statistics in brackets afterwards. Check with your supervisor about how to report statistics. Also check published papers! You should have read plenty by this point. Another pitfall to avoid is assuming that really small p values equal really important results. P values tend to get smaller when you have lots of data, so you can get a tiny p value but when you look at a scatter plot the points are all over the place. Instead look at r² values, a high r²value shows you how strong the correlation is between your variables (but again be careful as when you have very few data points r² are likely to be high).

10) So how do I get a 1^st class (A) mark?

Again see point 2 and check the marking scheme. However, most institutions will have broadly similar requirements. We want you to show us that you could be a professional scientist and that your thesis could be written up for publication with some extra work. This means we want to see the following: really clear links between your background information, aims, methods, results and discussion, critical evaluation of the methods you employed and the results you obtained (how could you do things differently?), excellent presentation throughout, clear understanding of how your project fits into the bigger picture and the wider literature, and evidence of novelty. Novelty is really hard to understand, but what we’re looking for is evidence that you engaged with the project and really began thinking like a scientist. This may be demonstrated by how you’ve linked your results with those of someone working in a different system or by excellent suggestions for how you’d further your project. We need evidence that you’ve gone above and beyond the advice of your supervisor and things you’ve learned in lectures and thought beyond the narrow confines of your project. It’s hard to explain what I mean, but when I see it I know instantly because I stop thinking of the project as the work of an undergraduate student and start thinking of it as the work of a future peer. Note that everything else must also be of a very high standard, so although you may show evidence of novelty in your discussion, if your presentation is a mess you will not get a 1^st.

Author

Natalie Cooper

nhcooper123

ncooper[at]tcd.ie

Photo credit

http://911thesis.blogspot.ie/

03/04/2013

Complementary colours

Any designer will tell you that choosing the right colour combinations are essential to strike the right tone and balance in a room, particularly if your goal is to attract clients. Well, what if your room is a web and your client is a moth?

This is just the situation the rather drab and dreary coloured Cyrtophora unicolor finds itself in. These spiders live almost exclusively on large moth prey, which are attracted by pale colours and twinkling lights, a problem if your evolution has led you to optimize your “I’m a brown leaf” appearance. Enter the small but enchanting Argyrodes fissifrons (a member of the dewdrop spiders). These spiders by contrast are endowed with a glistening silver and black pattern. These little guys face a rather different dilemma: they are kleptoparasites (food thieves!), meaning that they use the web of another larger spider species for feeding and reproductive territory.

Somewhere along the lines these two species found each other and struck up what is the first recorded example of an arthropod predator mutualism based on colour. Predator mutualisms, where both species benefit from the relationship, are rare due to conflicts of interest. Most dewdrop spiders live off the webs of others and suffer high levels of aggression from the hosts (somewhat understandably!). It was noticed however that A.fissifrons and C.unicolor seemed to coexist quite happily and that webs of C.unicolor even seemed to intercept more prey when A.fissifrons was present. The reason: The twinkling silver body of A.fissifrons. Against a leafy background the silver A. fissifrons is quite conspicuous and even attractive to the primarily visually oriented Hawkmoth prey. It is thought that the moths read the silver as some kind of a cue, potentially reflecting the moonlight at a similar intensity or wavelength as the stars, used by the moths for celestial navigation. These large moths however are much to big for little A.fissifrons to tackle; they prefer the smaller “accidental” prey. The result: These two species live quite contentedly side-by-side, one providing the house and the other the decoration.

Most animals that use colour signals use them as warnings, as mating indicators, service providers (as is the case in cleaner fish), camouflage and mimicry. If your ecological and evolutionary pressures demand a more low-key and less vibrant costume, adding a splash of colour from a friend with similar interests it seems may lead to joint benefits. Co-evolutionary related colour patterns, such as those associated with mimicry, usually arise from antagonistic interactions among species so it is interesting to see examples like these and wonder whether some might also arise from, or might eventually evolve as a result of, synergistic interactions among species.

Author

Deirdre McClean: mccleadm[at]tcd.ie

Photo credit

wikimedia commons

29/03/2013

Dinosaurs are useless if they don’t go in trees!

I’d like to ask the question many paleontologists have to face when they (foolishly) venture out of their museum storage: “So you’re studying fossils right? But what will that bring to the people? A cure for AIDS?”. There are many possible answers from a punch in the face to more mature responses. But I was recently asking myself the question from a biologist’s point of view: “What can biologists really do with the fossil record?”. Well obviously, we can use it to recreate and understand the history of our planet (like in Nature last week) or to do use some nice methods in trying to understand ancient ecosystems. People even might feel lyrical and do some serious work on paleo-poetry! But all of these guys are paleontologists right? They live in their museums and only go out for a movie once every 10 years… How about the other biologists?

Think about it, when ever you’re studying any organism, it is obvious (thanks to this bearded ape) that they had a 3.5 billion year history behind them. Ignoring that might lead to a misunderstanding? As an example, I’d like to use my favorite PhD-presentation example: the crocodiles. When we talk about crocodiles, we automatically think about the few species of big lizard that live in rivers in the tropical/sub-tropical latitudes. But, after a quick look at the history of our planet, the only description that is more or less correct is “lizard” (archosaurians to be more precise). Crocodiles are composed of many species (8 genera today – soon to be 6 – but >70 in prehistoric times) that lived in rivers as much as in the sea, on the ground or even sometimes in trees and in tropical to temperate climates (remains of crocs were found in Normandy – France).

Well maybe that’s just because of this group. But if you think about it, many other groups have ecological or evolutionary features that becomes truly astonishing once you take into account their full history. For my PhD I decided, with Natalie, to look at this fun fact (life existed before yesterday and the people studying it don’t always focus on dinosaurs) through primates. My idea is to combine extant data based on DNA with extinct data based on morphology to have an integrative tree of all primate history. I agree that this sounds a bit too easy and naive, (the method is a bit more complex) and I’ll probably end up with something more humble. However I think the primates can be a good example to illustrate the point about the hidden diversity among extinct groups. The primate fossils are not dramatically different than the extant once (unlike crocs, there were no pelagic primates) but they still show some really interesting features, for the macroecology side, combined extant and extinct primates show massive variation in body mass in some groups (lemurs) but very few variations in others (tarsiers). Or on the macroevolution side, such an integrative tree could provide some further understanding to the old debate of primate origins! Well at least I hope so. For now I’m just comfortable with eating some burgers with a diet coke and a gun in a pickup truck while I’m scanning some primates in the Smithsonian Institution in Washington DC.

Author

Thomas Guillerme: guillert[at]tcd.ie

Photo credit

Scott Hartman

http://www.skeletaldrawing.com/

27/03/201327/03/2013

Tyre Pressure

I’ve recently been spending a lot of time working with undergraduate students and marking their work and much of it has been on the subject of evolution and natural selection. This can be a difficult topic to clarify in the mind of younger students and it’s often difficult to recall specific examples which can be easily explained. Usually you have to come up with some hypothetical situation whereby some selection pressure drives a population towards evolutionary change. A newly published study in Current Biology by Brown and Brown however provides a beautiful (and more importantly brief) example of evolution and natural selection at work.

They have been studying populations of cliff swallows (Petrochelidon pyrrhonota) in Nebraska for almost thirty years, attempting to evaluate the costs and benefits of group living in these highly social birds. In an interview with John Dankosky lead author Charles brown explains how his habit of checking road killed birds for rings (or bands, as they are called in the US) led to an intriguing discovery. Firstly they noticed that over the years fewer and fewer birds were being killed on the roads (Figure 1), but also that these road killed birds tended to have longer wing lengths compared to individuals of the general population.

Figure 1. Change in wing length and number of road killed swallows (From Brown and Brown 2013).

So if you are a cliff swallow why does having a longer wing make you more likely to be run over by a car? Well it all comes down to the angle of escape. Birds with shorter more rounded wings are able to take off more vertically compared to individuals with longer more pointed wings, essentially shorter winged birds can get out of the way of oncoming traffic more quickly. It seems that this selection pressure from vehicles has been driving (I make no apology for the pun) the evolution of shorter wings in this population of cliff swallows.

Cliff swallows are migratory birds, travelling from South to North America annually and longer more pointed wings are generally seen as an advantage when it comes to long distance flight. Therefore it seems that the shorter winged individuals may pay an energetic cost compared to their longer winged conspecifics, but this cost may be outweighed by the benefit of being able to avoid traffic. Whatever the case may be I think this study provides a nice example of selection pressures steering morphological adaptations along the road to survival. Next time a student needs clarification on this I’ll remember, tyre pressure.

Author

Keith McMahon: mcmahok[at]tcd.ie

Photo credit

Tommie Kelly (www.tommiekelly.com)