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Seminar Series: Nathalie Pettorelli, Institute of Zoology, London

space monitoring

Part of our series of posts by final-year undergraduate students for their Research Comprehension module. Students write blogs inspired by guest lecturers in our Evolutionary Biology and Ecology seminar series in the School of Natural Sciences.

This week, views from Sharon Matthews and Sinead Barrett on Nathalie Pettorelli’s seminar, “Monitoring biodiversity from space: a wealth of opportunities”.

Space, the final frontier for ecology?

Okay, you got me.  I am a trekkie who is fanatical about anything space related. So when I saw that this week’s seminar was to do with conservation biology from space, I was hooked!  Dr. Nathalie Pettorelli from the Institute of Zoology, London spoke with passion and enthusiasm about a new wave of ecology; monitoring species and ecosystems from space.

We were treated to information about remote sensing and how data from satellites can be used to help ecologists in the tasks of assessing population size and habitat condition. Earth observation (EO) data is free and is ripe for the picking.  Satellites are able to “boldy go where no one has gone before” or very few people have (sorry, I will stop with the star trek quotes now!).  They can get information on places that are often inaccessible and inhospitable for the lowly researcher like Antarctica and the Sahara desert.

One of the major tasks ecologists face is estimating the size of a population.  Dr. Pettorelli talked about an ingenious research project that used information from satellites to gain an estimate of the population of emperor penguins (Aptenodytes fosteri) in Antarctica.  Emperor penguin populations may be affected by climate change in the next few decades due to changes in sea-ice distribution and therefore it is important to get an estimate of the extant population.

Frettwell et al. (2012) examined quick-looks from three different very high-resolution satellites.  These have a resolution of ~ 10m and are able to show great detail.  The researchers looked for staining on images and classified it as snow, penguin, shadow or guano.  When areas with penguins were identified, they analysed the penguin pixel area through regression equations.  The statistics gathered from this were used to convert the area of penguins to population numbers.

In this study, the identification of a penguin from a pixel area was done by human interpretation and this led to some error especially in areas of high guano staining.  This could be resolved with future development of higher resolution satellites.  However, there were other issues that arose from using this technology.  Researchers identifying penguins from pixels made an assumption that a pixel constituted one individual when it may in fact have been an individual with a chick close to it.  This can affect the estimated population size.  The kind of error association with using satellites makes me think that this satellite approach should be backed up with other methods such as field study where possible.

Remote sensing can allow research to be undertaken over a broad spatial and temporal scale.  One of Dr. Pettorelli’s projects involved using EO data to assess a game reserve in central Chad for its ability to sustain a reintroduction of the Scimitar-horned Oryx (Oryx dammah).  A vegetation index (an indication of ‘greeness’) and annual mean precipitation, were assessed over a 27-year period for this game reserve. The results showed that precipitation was a main driver of vegetation dynamics and there was an intense greening in the south of the region.  Dr. Pettorelli also found that there was a contraction of the transition zone from north to south. This was an area that was identified as most suitable for the oryx.  This study showed how remote sensing can help inform ecologists about variation in a region over time.  It can greatly enhance the success of reintroducing a species into a suitable area.

There is no doubt in my mind that data from remote sensing can help ecologists in their work but I don’t think it should be used in isolation. Ecosystems involve a complex mix of interactions of many variables. Therefore, this approach could be used alongside other tried and tested (down to earth) methods of studying ecosystems and biodiversity.

Author: Sharon Matthews

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Evidence of Global Change is Sky High

As we all know, climate change is affecting the world in which we live. One aim of scientists is to find out the extent of this change. At a seminar given recently in Trinity College Dublin, Dr. Nathalie Pettorelli from the Zoological Society of London informed us about a new method of doing this. With benefits including the cost, its sustainability, reproductivity and standardised information, satellite usage as a way to monitor biodiversity seems like an excellent option.

Dr. Pettorelli mentioned the vast array of options of satellites available for monitoring depending on what you want to find out in the study. For example, very high resolution imagery has been used in order to count penguins in colonies, Landsat has been used to study the gorilla habitat in Virunga and LiDAR satellites which give a 3-D image have been used in the Bavarian forest. But what interested me most was when Dr. Pettorelli mentioned the ability to monitor vegetation indices and how this technique was used in the reintroduction process of the Scimitar-horned Oryx in Ouadi Rimé-Ouadi Achim Game Reserve in central Chad.

The Scimitar-horned Oryx was last found in the wild in the 1970’s. However it has been kept in captivity and there were plans of reintroducing it back into this area in central Chad. In order to do so, a habitat assessment was undertaken to establish whether the area would still be suitable for the species to live in. The primary productivity over the past number of years was viewed using remote sensing (satellite) techniques. It was seen that the vegetation in the north had significantly dried while the area to the south showed intense greening. Because the Oryx lives preferably in sub desert regions, suitable habitat here was declining and it was not advised to reintroduce this animal to the area.

To me, this shows just how important this method of monitoring is. Due to the increased changes that come about as a result of climate change, species are no longer suited to their natural habitat. Although it wasn’t mentioned in detail in the seminar, it struck me that one use of this satellite method of monitoring would be to use it in assisted migration. This is a method of conservation that involves humans undertaking a translocation of an animal or plant species. This is used when a species can no longer survive in their habitat and so must be moved to a more suitable area. This method of conservation is debatable as there are many associated risks involved including the impact on original species in the new habitat. However, with scientists doing research on this to study possible effects, it may save a species from dying out. Suitable habitat needs to be found for assisted migration to work. The methods that Dr. Pettorelli uses in her habitat assessment in central Chad could be the ideal way to find these habitats needed. This highlights the need for this new method of data collection. Because it is done at such a big scale, it seems like an excellent way of finding large habitats suitable for a new species, whether it’s a tree or a large carnivore.

Changes are occurring globally as a result of anthropogenic actions, and species worldwide are dying out as a result of this. It is clear from the numerous examples mentioned at the seminar that there are many uses of satellite imagery in monitoring biodiversity worldwide. After hearing Dr. Pettorelli talk about this subject, I left realising just how important technology such as satellites are in a time when global change is sky high.

Author: Sinead Barrett

 

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Please consider this a polite spanking

peer_review

The recent hilarious #SixWordPeerReview hashtag on Twitter got me thinking about the first ever review I got for my first ever paper (thanks @Phalaropus for the reminder!). I thought I’d share it here (and if you want to see if you agree with the reviewer, the paper was eventually published in Global Ecology and Biogeography: Cooper et al 2008).

As a bit of background, I collected lots of data during my Masters project on life history traits of amphibians and then looked at macroecological correlates of clutch size, body size and geographical range size, and also at how these variables correlated with IUCN Red List status. My dataset contained over 600 species of amphibian – pretty much all the species I could get hold of data for at that time. Here are the “best” comments from the reviewer (the whole review was two pages long so I’m not reproducing the whole thing). My favourite comment was at the end.

“the study was done on less than 10% of the appropriate species […] Such academic laziness is inexcusable and scandalous”

“there are many instances where the authors appear to pull the wool over the reader’s eyes”

“It is a strong reflection of the workers to submit such a poorly conceived and obvious “quick and dirty” first stab at something that needs to be taken much more seriously”

“the clear misinformation in the abstract […] is obviously the kind of positive spin more associated with politics than science.”

“Who would be fooled by such tricks as claiming that data on <10% of amphibians is “large”. Certainly not this reviewer.”

“Without even a cursory explanation for such an egregiously low sampled diversity, it is hard to glean any merit at all from this study.”

“How can sane scientists think that <10% of the diversity would be sufficient to advocate involved analyses and draw conclusions?”

“This is another example of embarrassingly obvious laziness.”

“That goes beyond even forgivable bending of the truth”

“If any of the authors were thinking, they would have realized that ALL of the reasons to do a phylogenetically corrected analysis are not met by their data. In fact, if there was ever a gross and more ill-conceived reason to NOT do a phylogenetically corrected analysis, this would be the dataset to do so on.”

“Errors in basic addition are another serious embarrassment” [FYI the maths was fine, the reviewer made the error not us!]

“I could go on, but I think that it is not worth my time at this point to find more problems (there are still many other issues the authors should go back to first principles on)”

[And finally the crowning glory of all the comments I’ve ever received in a review]:

“Please consider this a polite spanking.”

As a first year PhD student this obviously upset me. But after a quick cry, a slice of Battenberg [cake], and a couple of pints of cider I was able to see the funny side! I still keep a print out in my office as a reminder that even when I get a bad review, it can never be as terrible as my first review! I’ve never worked out who the reviewer was, but as the editor said they were clearly having a bad day! I hope things got better for them! This review also reminds me to always write constructive comments, especially for PhD students, and if I don’t have anything nice to say I write a short review rather than airing all my grievances in print!

Author: Natalie Cooper, ncooper[at]tcd.ie, @nhcooper123

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Seminar Series: Redouan Bshary, Université de Neuchâtel

cleaning station

Part of our series of posts by final-year undergraduate students for their Research Comprehension module. Students write blogs inspired by guest lecturers in our Evolutionary Biology and Ecology seminar series in the School of Natural Sciences.

This week, views from Cormac Murphy and Gillian Johnston on Redouan Bshary’s seminar “Marine cleaning mutualism; from game theory to endocrinology and cognition”.

To clean or not to clean that is the question

With an average size of around seven and a half centimetre I would never have considered the  blue streak cleaner wrasse, Labroides dimidiatus, to be a particularly intimidating animal. Yet over the course of 50 minutes I heard them compared to 4 of the most villainous and screaming entities I know; Niccolo Machiavelli, the Mafia, the global market and a four year old child (anyone surprised by this last entry has probably never had to take care of children).

Cleaner wrasse gain much off their food by eating off the bodies of larger client fish that visit their cleaning stations. This would seem to be a mutually beneficial arrangement, the wrasses have their food come to them and the client fish have their exoparasites removed. But the cleaner fish face some problems. While there are local clients that guarantee a meal, visitor fish passing through the area (who are bigger than the locals 80% of the time) are not as willing to wait in line to be cleaned and will move on. The cleaner client relationship is strained by the cleaners’ preference for the mucus the fish makes rather than the exoparasites. But taking the yummy mucus requires biting the client fish, who may retaliate and will definitely leave the cleaning station after such an encounter. The matter of obtaining food from the most readily available sources and/or of the highest nutritional content is of special importance to the wrasse. Once a wrasse has gained a certain amount of body mass it becomes a male and may take over a harem of smaller females, giving it a greater chance of bearing more offspring. This is something to strive for, but for the wrasse that are already males they don’t want one of their harem to become one of their competitors.  The males will attempt to cheat before the larger females can deprive them of the nutritious mucus and will retaliate against the larger females if they cause the clients to jolt and leave. Dr. Redouan Bshary of the Université de Neuchâtel, Switzerland, is interested in how these little fish deal with the dilemmas they are faced with in their struggle to acquisition food for power and their aggressive gender politics.

An example of Dr. Bshary’s examinations of the cleaner’s feeding strategies focused on their response to visitors. This was tested by placing the fish in a tank with two plates of food, a green one representing the local client and a pink one representing the visitor. If the fish ate off the pink plate, both plates would remain and the fish would get all the food. However, if the fish ate from the green plate first the pink plate would be taken away, simulating how a visitor fish moves on if it doesn’t get cleaned on the first approach. This task was deceptively difficult, as unlike classical conditioning i.e. Pavlov’s dogs, the fish get a reward whichever plate they go for, the behavioural learning lies in realisation that one option will result in a future benefit (both food plates remaining) in addition to the immediate reward. The majority of adults tested learned to go for the green plate first within 100 trials. Juvenile cleaners could not grasp the lesson with the exception of one individual, though it turned out that particular juvenile was just very fond of pink and when the experiment was repeated with the colours reversed it was just as lost as its peers. The adult cleaners’ ability to modify their behaviours based on previous trial experiences are impressive when you consider that the fish outperformed both great apes and human children under four years old that were given the same task.

This is just a snapshot of Dr. Bshary’s work on the behaviour of cleaner fish which brings up interesting and controversial questions about the intelligence of these animals and the conditions under which more complex forms of cognition might develop. Does the cleaner’s besting of our infants suggest they have a higher level of cognition or, more likely in my opinion, are their actions the result of interacting evolved rules of thumbs? Studies like this show us that animal behaviour can be far more complex than it may originally appear.

Author: Cormac Murphy

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You Should Never Bite the Fish That Cleans You!

On Friday the sixth of December, Redouan Bshary came to Trinity College to deliver what turned out to be a lively talk accompanied by engaging slides that summed up the last ten years of his work! Along to his talk, he brought an abundance of enthusiasm, leaving us all in a jolly mood to start our weekends. Aside from the upbeat approach to his talk, other aspects captured the audience’s attention as well. The aim of Bshary’s work turned out to be very interesting and was a very appropriate topic to discuss with a group of zoology enthusiasts.

The aim of Bshary’s research was to discover whether it is easier for cleaner fish to use size over any other characteristic in order to distinguish between resident and visitor fish. Visitor fish tend to be bigger and this can help cleaner fish to make quick decisions, which can improve their fitness instead of wasting time, allowing visitor fish to move elsewhere.

Cleaner fish provide a service to larger fish that consists of removing dead skin and parasites from their bodies and in some cases, removing particles from their teeth. The ability for them to quickly distinguish between visitor and resident fish in order to provide this service is very important, so the fish invest a lot of time in trying to learn this skill. If the cleaner fish make the mistake of feeding from the resident fish first, by the time they move on to the visitor fish, it will have moved elsewhere, giving other cleaner fish the opportunity to feed from it. This reduces the amount of food available to the cleaner fish.

Bshary tested the efficiency with which cleaner fish can learn this skill of feeding on the visitor fish first. He set up his experiment using a cleaner fish placed in a tank with two plates of food, each plate being a different colour. One plate represented the visitor fish, the other represented the resident fish. He allowed the cleaner fish to feed from whichever plate it desired. If the cleaner fish chose to feed from the ‘visitor’ plate first, it would then be allowed to feed from the ‘resident’ plate afterwards. However, if the fish selected the ‘resident’ plate first, by the time it was finished, Bshary would have removed the ‘visitor’ plate. Bshary repeated this experiment for 100 trials in order to establish how quickly the fish learned to associate feeding from the ‘visitor’ plate first with the availability of more food.

During his talk, he presented his results on graphs and explained their significance. His study found that, on average, adult cleaner fish could learn to do this after fifty trials, with juvenile fish taking significantly longer. He then slightly modified the technique for this study and tested it on other species. He found that humans were capable of learning this, but not until they were at least four years old. He found that chimps were slightly better at it but still not at all as efficient as the cleaner fish. He concluded that this is quite a difficult skill to learn so the fish must be in someway adapted for this task. It is obviously useful to them so perhaps this adaption has evolved to increase their fitness by obtaining higher amounts of food. The ability to learn this task so quickly has established that cleaner fish have quite a high cognitive ability.

Given that there is intense competition in the reefs where the cleaner fish are found, it is important that they invest effort in distinguishing correctly between visitor fish and resident fish.

Using size as a proxy, cleaner fish correctly identify visitor fish 87.5% of the time but this obviously is not good enough as the fish then spend time learning to properly distinguish, allowing them to be correct 99% of the time.

Bshary emphasised the important roles that cleaner fish play in the well-being of larger fish and vice versa. Trust is very important between the two, especially when cleaner fish will often venture into the mouths of larger fish to clean their teeth. Honesty is essential for these dynamics to work and so larger fish will open their mouths as an honest commitment signal, reassuring the cleaner fish that this is a safe way of getting food. Should the larger fish try to eat the cleaner fish, upon closing its mouth, the water will be expelled out, bringing the cleaner fish with it. Before Bshary’s talk, I had often seen examples of smaller fish in the mouths of larger fish and wondered how they could be so trusting, this informed me that really they were not in danger at all.

Overall, Bshary’s talk was engaging and provided answers to questions that I had asked myself in the past. If it were up to me, he would certainly be a welcome speaker at Trinity College again.

Author: Gillian Johnston

Image Source: Wikimedia commons

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Levels of Selection

Okasha 2006

Thanks to the magical (and sometimes frustrating!) technological capabilities of Google+, every fortnight we have international phylo/macro journal club meetings which span three continents and even include elements of time travel (the Australian participants are always in the future!). Among the varied topics we cover, one of our recent sessions was a discussion of Samir Okasha’s book, Evolution and Levels of Selection. Evolutionary biology is an empirical science which also receives attention from philosophers. The two approaches are often difficult to reconcile so Okasha’s book is a welcome bridge for the gap between philosophical theory and practical biology. We mainly focused on the chapter which deals with species selection, clade selection and macroevolution and addresses the units of selection debate.

As a brief background, the debate hinges on the unit(s) and level(s) at which evolution by natural selection operates. Biological structures are inherently hierarchical. As researchers we tend to focus on specific organisational levels, so community ecologists will have very different concerns and interests to cell biochemists. Biological structures are shaped by evolution but the question is at which level(s) in the biological hierarchy does natural selection act? The theory of natural selection is an abstract concept; as Lewontin describes, the tripartite conditions for evolution to occur are phenotypic variation, differential fitness and heritability. So which level of biological organisation satisfies these requirements? Well it seems like it depends on who you read and who influenced your evolution teachers!

In the UK and Ireland we are generally taught evolution from a gene-centric point of view – the Dawkins school of thinking in which selection acts at the level of the individual and the unit of selection is the gene, and only the gene. However, across the pond, there seem to be more proponents and acceptors of higher or multi-level selection theory; the idea (following Stanley, Gould and Eldredge among others) that natural selection is not restricted to genes as the sole units of selection. It’s a confusing debate, especially when it comes to teasing apart the concepts of levels and units of selection; Okasha argues that a gene’s-eye view (genes as the units) can still be adopted for selection acting at various hierarchical levels. Furthermore, concepts of species level selection tend to become confused with group selection – a notoriously controversial concept which is guaranteed to set alarm bells ringing for many people.

Returning to Lewontin’s criteria, the basic idea of species level selection is simple. If species vary in some sort of traits and that variation gives rise to differential extinction or speciation rates, then some types of species will become more common than others. This approach is particularly common from palaeontological or macroevolutionary perspectives. If you’re interested in long-term evolutionary trends such as patterns of differential lineage abundances or extinction and speciation trends, it’s intuitive to treat the species as the level at which selection acts. This highlights a fundamental component of this debate: the gene-only-level of selection is usually advocated by microevolutionists; those who are interested in changes at the genetic level. In contrast, multilevel selection theory receives support from macroevolutionists who, due to their fundamentally different approaches, consider individual species to be their smallest units of interest.

When you think about species selection it is often easy to confound it with clade selection yet Okasha draws a clear distinction between the two concepts. Clades are, by definition, monophyletic; comprised of a single ancestral species and all of its descendant species. Unlike species, clades cannot split to create new clades with ancestor-descendant relationships because any new clade will inevitably be nested within the old clade (the diagram in Okasha’s book makes all of this far clearer than my description!)

Figure
Clade A is part of the larger clade B but it is not the offspring of clade B (offspring must have an independent existence from their parents and be able to outlive them).

Speciation and extinction rates are clearly not uniform; some lineages radiate into many different types of species which enjoy happy evolutionary lives (think of our arthropod-dominated world) while other evolutionary lineages produce fewer species. The question is whether these patterns are the result of species-level, macroevolutionary processes or whether emergent, species-level properties can be explained from selection acting at the genetic level. As an “acid test” for genuine species selection, Okasha proposes Elizabeth Vrba’s view that species selection must in principle (though not necessarily in practice) “be able to oppose selection at lower hierarchical levels”. Otherwise species level selection merely describes processes which can also be explained from a genetic-selection stance. For example, species selection may have been involved in the evolution or maintenance of sexual reproduction; the advantages of sexuality at the species level may have outweighed the two-fold cost of sex at the individual level and therefore favour the evolution of sexual over asexual lineages.

However, there seems to be a general paucity of clear examples which conform to Vrba’s acid test. One intriguing suggestion as to why this may be the case is time. The generation times of species producing new lineages are clearly far longer than the generation times of individuals’ reproduction so perhaps comparatively sluggish species selection processes have not had sufficient time to oppose evolutionary patterns which arise from individual selection?

Confused? It’s an interesting debate but certainly not one for the faint hearted and the fact that each philosopher/scientist/punter on the street seems to have jargon and slightly differing definitions of their own only serves to  cloud the murky waters further. It is, however, interesting to contemplate how our own research backgrounds and the inclinations of our teachers influence our approach to the debate. If you’re interested in these kinds of questions then Okasha’s book is well worth the read or else you could join in with our Phylo/Macro journal club meeting; wherever you are in the world we’re on a Google+ hang out near you!

Authors: Thomas Guillerme (guillert[at]tcd.ie, @TGuillerme) and Sive Finlay (sfinlay[at]tcd.ie, @SiveFinlay)

Image Source: Okasha 2006, Evolution and the Levels of Selection

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NERD club transferrable skills: reviewers, rejections and responses

peerreview

Academic publishing: the currency of any research career. It’s all very straightforward; take your most recent ground-breaking results, wrap them up into a neat paper, choose the perfect journal, allow said paper to persuade an editor and reviewers of your brilliance and bask in the reflective glow of getting your research out into the world. Whether you see this rosy scenario as a target or delusional and unattainable aspirations, things rarely work out so smoothly. Instead, every researcher must learn to deal with the topic of one of our recent NERD club discussions; reviewers, rejections and responses. As a collective of staff, postdocs and postgraduate students, here are our thoughts on the dos and don’ts of dealing with the three r’s of academia.

1)     Reviewers

Some journals invite authors to suggest reviewers or editors for their papers. If this happens, pick who you think is the “best” person whether that’s because the person is an expert in your field (although see our final point below), likely to give a fair review or because they are familiar with your work. Only suggest people to be reviewers if they have published themselves i.e. aim at the level of senior graduate student or from post-doc upwards. It’s also a good idea to choose someone that you’ve cited a lot in your manuscript (no harm to get on their good side). Equally, if you gave a conference talk recently, remember that person who seemed so interested in and enthusiastic about your work in the pub afterwards – chances are that they might be a fair and favourable reviewer. We also thought that, if you feel it’s necessary and you have a good reason, it might be a good idea to make an editor aware of people who you would prefer not to review your paper. However, be warned of the rumours that some editors may prefer to ignore such preferences and deliberately choose people from that “exclusion” list as reviewers.

In contrast, when selecting potential reviewers or editors, don’t choose someone who you have thanked in the acknowledgements of your manuscript. These are usually people who helped out or offered advice at some stage during the research so they would have a conflict of interest when it comes to reviewing the manuscript. Of course, you can also use this guideline to your advantage by seeking advice from and therefore acknowledging people who you definitely want to avoid as potential reviewers… Also from a conflict of interest point of view, don’t suggest your main collaborators, close friends or people from your own institution as potential reviewers. Similarly, for obvious reasons, don’t choose someone as a potential reviewer if you know that they dislike you or your work!

Once you have considered all these points, our final piece of advice about choosing reviewers or editors is don’t get hung up on it! Your preferred reviewers may not accept the manuscript, particularly if they are the senior, time-limited experts in your field. Finding reviewers for a manuscript is ultimately a lottery so, having thought about a few of our suggested guidelines, there’s no point in agonising over the process too much.

2)     Rejection

It’s never pleasant to think about but your chances of rejection in all aspects of academia are high. Rejection of a manuscript can be particularly disheartening as it represents a dismissal of months if not years of your hard work. Our main piece of advice is not to do anything hasty. However unfair, pedantic or ridiculous the reasons which “justify” the rejection may initially seem, their bitter sting usually mellows if you take the time to sleep on it (after getting cross and having some comfort food/drink/other activities…). Similarly, don’t ruin your Friday evening/weekend/holiday by obsessively checking your emails for an editor’s response which will more likely than not be negative.

After hopefully returning to a somewhat more rational state, try to take the reviewer’s comments on board. The constructive ones will help you to make a better paper and parts which reviewers didn’t understand are often because you could have clarified your points better. Ultimately, it’s important to be realistic; the chances of rejection of a manuscript are high so be prepared to resubmit elsewhere (think back to our previous advice about working down the list of journals for which you feel your paper is suited). You could even have another version of the paper drafted and formatted for the next journal on your list even before you receive a response from your initial submission. It may take an initial investment in time and energy but at least the next version of the paper is then ready to go if you’re unlucky enough to receive a rejection from your first journal of choice.  The most important advice to emerge from our discussion was to be thick skinned and not to take rejection personally. You can’t publish without experiencing rejection so it’s important to share your experiences (both good and bad) and to listen to the advice and woes others. You’re not alone!

Our final cautionary point was that you don’t necessarily have to accept rejection. If your paper was rejected on the basis of reviews which you think were poor, biased, unfair or just completely off the mark, it might be worth arguing your case with the editor and/or reviewers. HOWEVER, only take up this tactic in exceptional circumstances where you have a VERY strong case to back up your points. If you get a reputation for being petulant, argumentative, obstinate or just downright rude it can only serve to seriously aggravate an editor and damage your future publishing prospects if not your wider research reputation.

3)     Responding to comments

Hooray! You’ve got through the reviewing gauntlet, dodged the cold blow of outright rejection and now there are just a few reviewers’ comments standing between you and potential publication glory. We came up with lots of dos and don’ts for how to deal with reviewers’ comments.

Most importantly, be polite and positive. No one was obliged to review your work so thank the reviewers for their comments and suggestions and consider adding them into the paper’s acknowledgements. Never be aggressive or rude and only write responses which you would be happy to say to a reviewer or editor face to face. Respond to all comments, no matter how trivial they may seem and show that you’re willing to make more changes if necessary. Don’t just ignore the bits that you don’t agree with. Show the editor that you have dealt with every comment by cross referencing the changes you made to the manuscript. To do this, either refer to the revised line numbers or, more preferably, cut and paste the sections that you have modified into your responses so that the editor doesn’t have to keep moving among different pages to check what has been changed.

Being polite and positive doesn’t mean that you have to be a push-over. If you receive a comment which is impractical, beyond the scope of your paper or just downright wrong, argue your point (with legitimate back up) but always retain a courteous tone throughout. If you have to deal with a whole slew of comments which are particularly off the wall or aggravating, ask someone to read your response before sending them to the editor – it’s always easier for someone else to pick up a passive aggressive tone which, despite your best efforts, may have crept into your writing.

If reviewers disagree on a particular point, either justify the changes you have made (don’t just ignore one reviewer’s comment) or your reasons for not making any changes. Don’t feel obliged to do everything that a reviewer suggests. Don’t ruin the flow of your text with awkward sentences which were clearly just inserted to please a particular reviewer. If you have good reasons (not just stubbornness or obstinacy) for sticking to your original ideas then make them clear.  Remember that you can always get in touch with the editor if you get unrealistic or conflicting instructions or if you’re unclear about what you are expected to change.

So there’s our collective field guide to the trials and tribulations of academia. They’re by no means exhaustive but they’re definitely a good starting point. However, as academic publishing seems to require good fortune and timing as much as scientific rigour, research merit and an eye for a good story, there’s no magic formula for how to succeed, no matter how carefully you follow NERD club’s collective wisdom…

Happy publishing!

Author: Sive Finlay, sfinlay[at]tcd.ie, @SiveFinlay

Image Source: justinholman.com

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Seminar Series: Kendra Cheruvelil, Michigan State University/Queen’s University Belfast

landscape limnology

Part of our series of posts by final-year undergraduate students for their Research Comprehension module. Students write blogs inspired by guest lecturers in our Evolutionary Biology and Ecology seminar series in the School of Natural Sciences.

This week, views from Kate Purcell and Andrea Murray-Byrne on Kendra Cheruvelil’s seminar “Understanding multi-scaled relationships between terrestrial and aquatic ecosystems”. (See Kendra’s blog about her trip to TCD).

The Power of Knowledge

As the old saying goes: “knowledge is power”. As scientists, a comprehensive understanding of that which we are studying is the key in enabling us to implement our research in a practical manner. From the perspective of an ecologist, compiling a large dataset can be costly – both in time and money. However the benefits of having a centralized dataset can be invaluable. Dr Kendra Spence Cheruvelil, an associate professor at the Michigan State University, has carried out extensive work on lakes in Michigan. Her work highlights the importance of compiling knowledge into shared datasets.

Cheruvelil recently gave a seminar in Trinity College on her work on Michigan lakes. Cheruvelil explained how data on the lakes in Michigan from governmental departments is not standardized. The data can therefore be used to draw incorrect inferences about the lakes in question. This example highlights the need to have a collaborative database where such information can be shared.

As well as explaining the need for a complete, standardized dataset, Cheruvelil demonstrated the importance of understanding the regional spatial scale when extrapolating information to make inferences about lake systems. Cheruvelil and colleagues stated the importance of fully understanding systems from the local to the continental scale. According to Cheruvelil, in order to make correct inferences we need conceptual models of relationships across scales, large datasets, and robust modeling approaches to deal with these data.

Cheruvelil and colleagues studied 2,319 US lakes in 800,000 km2. Using two variables – total phosphorus and alkalinity – they found that there was a high level of among-region variation in lakes. The found that the amount of regional variation present depends on what you look at, and as spatial extent gets bigger so too does regional variation. The amount of regional variation therefore depends on the spatial extent, the response variable of interest (with total phosphorus < alkalinity) and the regionalized framework.

Why is knowing what drives ecosystem processes in lakes important? Cheruvelil made the point that having these data allows for interactions between local and regional scale variables to be accounted for. Inferences can then be made about these variables and how they may drive ecosystem processes in other lakes with less data. The landscape features driving lakes are multi-scaled (local and regional), both hydro-geomorphic and anthropogenic, difficult to disentangle and different according to the response variable of interest.

Cheruvelil’s research is important, especially from a management point of view. It shows the importance of using both local and regional scales when making inferences about any ecological system, including lake systems. Making better and more informed inferences about the driving factors behind the lakes are especially important as we’re in an era facing large-scale climate change.

Author: Kate Purcell

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Paint by numbers: using inferences as a guide to paint the bigger picture

Limnology is the study of inland waters, including lakes, rivers, streams and wetlands. Dr Kendra Cheruvelil is a landscape limnologist currently carrying out research on a huge dataset of lakes in the US. She began her talk by discussing the implications of this kind of work. Her research attempts to integrate freshwater and terrestrial landscapes. As she pointed out – the map of an area you choose to show depicts exactly what you want someone to see. She illustrated this point by showing different land use maps for the state of Michigan. Michigan looks like quite a dry place when you only include lakes on the map, but when streams and wetlands are also included the picture of the freshwater ecosystem is very different!

Cheruvelil compiled a huge multi-scaled (local and regional) and multi-themed (like geology and land use) dataset from existing databases.  These databases came from different organizations and in total she ended up with data on 2319 US lakes in a 800,000km2 area. This huge dataset was necessary for her equally big questions. Firstly she asked how much among-region variation is there, and secondly she wanted to know what the likely causes of this variation (if any) were.

Because ecosystem variation is driven by things like hydrology, geomorphology, as well as anthropogenic and atmospheric factors, on different temporal scales like decadal or seasonal, and different spatial scales like local or regional, the research area can be quite messy in your head (at least it was in mine!) but Cheruvelil broke it down nicely and made it a lot more digestible.

Two variables she chose to look at were total phosphorus and alkalinity. These were chosen as they can indicate stressors: total phosphorus as it can show eutrophication, and alkalinity as it can indicate acidification. They also provide a nice contrast as total phosphorus is considered to be important on a small scale, whereas alkalinity is broader as it has to do with geological features. Using hierarchical models to test the data (which I won’t dwell on because it’s a little above my head!), Cheruvelil found that a high proportion of variation is regional, for example about 75% of the variation in alkalinity was regional. This did, however, vary depending on which regionalization framework she used, but she picked a hybrid model that encompassed both freshwater and terrestrial factors, so despite the different results depending on the framework I think she gave good reasons for picking the one she eventually used.

As far as her second question – the likely causes of this among region variation – she tested the data with conditional hierarchical models (which again I won’t go into, but neither did she which was for the better I think!). Results here suggested that a few regional variables explained a high proportion of the regional variation. However, she was careful not to jump to conclusions that these variables were driving among region variation, and she clearly explained that there are most likely some confounding variables which are hard to disentangle using her methods.

Okay, so you want to study all these lakes and see if they vary among regions – but why? Why on earth is this important? These are valid questions that you may be asking yourself – and questions Cheruvelil was prepared for. She explained how making inferences from a sample lake is important when considering the bigger picture, for example when going from a local level of an individual lake and its watershed to the regional level of grouped lakes within a similar geographical region, to finally all the way up to a continental scale. The void she is filling with her research is the regional level – building models that will allow future researchers to extrapolate from their study lake and infer things at broader scales to see the bigger picture. This is important as most studies on ecosystems will be on a single lake, and I think the take home message was that findings at the local scale may or may not apply to other lakes, depending on how similar they are and if they are in similar regions.

Author: Andrea Murray-Byrne

Image Source: Landscape limnology research group http://www.fw.msu.edu/~llrg/

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Science and Journalism

sciencejournalism

As scientists with access to hundreds of peer reviewed journals its easy to forget that we are a privileged bunch. We get to read science straight from the horse’s mouth without anyone to get between us and the research. Yet for the majority of people journals are hidden behind paywalls and even open access journals remain largely the domain of working scientists if for no other reason than reading scientific journal articles is hard work. They demand a high level of prior knowledge and often use terms that are completely meaningless to anyone outside their field. It’s no surprise that the majority of people get their science news from newspapers.

The problem with science in newspapers is that it’s really badly done. It’s often based on press releases from universities and others have written about how the media will take a story and run in whatever direction they please, regardless of the actual research. Science journalism has been relegated to the side-lines. While it would cause outrage if someone who knew nothing about football was allowed to write in the sports section, non-science journalists are regularly writing science stories, unable to critique the work or put it in any context. On the one hand it leads to sensationalist stories but on the other it can result in the real news story being buried among trivialities (something I’ve written about before).

It’s one thing to disagree with a news story about your own research but what about other science stories? If you have any interest in science chances are you’ve read a news story and shook your head in disbelief at the poor reporting. You may have moaned about it to friends until they wondered off saying something about “letting it go” or “getting a life”. But what, really, can you do? You’re just one person. . .

Well, it turns out there is something you can do. You can email the journalist. You can explain, politely and calmly, exactly what was wrong and then suggesting ways of making the story better. So, rather than say;

“Your article was rubbish, you don’t have any idea what you’re on about it was all wrong!”

you could write,

“I was disappointed by your article. You said that whales are a fish when they are actually mammals”.

(Hopefully you won’t see any errors that egregious!)

You may be thinking that it’s all very well and good to email them, but why should they listen? Why do they care? The story’s finished, they’ve moved on. Well, one reason is that most stories are online where they form a permanent record, so any errors will remain forever unless corrected which does nothing to help a journalist’s reputation. Secondly, most of the errors aren’t out of spite or even callous disregard, it’s because they don’t know any better. As I said, a lot of science journalists aren’t experts so they’re going to make mistakes. Even if do have a background in science they can’t know everything. Could you write as well on quantum mechanics as you could on evolution, for example? I doubt it.

This all sounds wonderful. You see an error in a science story, you email the journalist and he corrects it and everyone goes merrily on their way. Really? Life isn’t that pleasant. Well, actually, it can be. The inspiration for this post came from an article I saw hyperbolically titled “New species of terrifying looking ‘skeleton shrimp’ discovered”. The original article gave no information about who had discovered the animal or why it was important. It also had incorrect formatting on the genus and family names. I emailed the author and politely explained the problems. I had a lovely response and he corrected the formatting errors, added the information it lacks and, most importantly, gave credit for the discovery where it was due. The article now online is the amended one and while still not brilliant, is much better.

The moral of this story is that if you see bad science in the news contact the journalist. Chances are they don’t know they’re making mistakes and as long as you are polite and specific they will heed your advice. While you won’t get a 100% success rate, or even a 100% response rate, you will get some response. Focus on the smaller articles usually written by people low down the hierarchical food chain who are most receptive, who haven’t been jaded and welcome polite, constructive advice and can be encouraged to do better in the future. If we all make the effort to correct bad science reporting we can hopefully help journalists and improve science understanding in the public domain. Not bad for one email.

Author: Sarah Hearne, hearnes[at]tcd.ie, @SarahVHearne

Image Source: blogs.discovermagazine.com

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Seminar Series: Fiona Doohan, University College Dublin

wheat field

Part of our series of posts by final-year undergraduate students for their Research Comprehension module. Students write blogs inspired by guest lecturers in our Evolutionary Biology and Ecology seminar series in the School of Natural Sciences.

This week, views from Gina McLoughlin and Joanna Mullen on Fiona Doohan’s seminar, “Plant-Microbe interactions – the good, the bad and the ugly”

GM Crops Don’t Kill

Genetically modified (GM) crops, are crops that have been modified using genetic engineering techniques to introduce certain qualities, or traits into a plant where they did not occur naturally. Usually, the genes for the desirable trait are taken from one plant and inserted into the genome of another strain of that plant. However, because of this engineering many people think that GM crops pose a serious health hazard and there seems to be a lot of tension around the topic of GM crops. This tension is mostly stemming from big companies, like Monsanto, that have nasty practice records and design GM crops for patents and profits instead of solving food problems.

However, there are many researchers out there that are working on GM crops to try and solve food problems and ensure there is enough food to feed the world’s growing population. Dr Fiona Doohan is a senior lecturer in the School of Biology and Environmental Science, UCD and she has been doing research on food security. The work that she presented to us in her lecture focused on how to enhance disease resistance in cereal crops. For her research she specifically looked at the disease Fusarium head blight (FHB) in wheat. Wheat is the second largest source of calories, after maize, yet it is produced in only a small percent of the world. FHB is a huge problem for farmers as it causes serious yield loss, which they cannot afford. It cost about €9 million per year in order to control FHB with inconsistent fungicides, so Doohan and her team are looking at a better alternative to protect these crops.

Deoxynivalenol (DON) is a mycotoxin that commonly causes the damage associated with this disease. DON is toxic to humans, animals and plants (Rocha et al., 2005) and it is very important that it doesn’t get into the food chain. DON also aids the spread of the disease in wheat heads and increases the severity of the symptoms of FHB (Bai et al., 2001). It causes bleaching of the wheat heads, alters membrane structures and causes cell death. DON also inhibits seed germination, shoot and root growth, root generation and protein synthesis (Rocha et al., 2005). Some wheat strains are resistant to DON and the genes that cause this resistance are being identified (Walter et al., 2008).

Doohan and her team wanted to look at different strains of wheat and how they reacted to DON. They put two strains of wheat up against each other, Remus and CM82036, to try to find the mechanism that allows DON resistance. Remus is the strain that is used in cultivation because it has more desirable qualities than the CM82036 strain but it is susceptible to DON. Analysis of the results was performed using DDRT-PCR and microarrays and a list of genes that could possibly be involved in DON resistance were obtained. One of the genes in this list was an orphan gene. This is a gene that had no significant homology to any known genes and it has also never been described before. Doohan and her team are doing further research into this orphan gene and hopefully it will be a lead to adding resistance to the Remus strain.

Doohan’s work may be essential to human survival if the population keeps rising and people need to start trusting research and open their minds to GM crops. Research has found that there are no adverse affects to using GM crops and they are no more unsafe than crops modified using conventional improvement techniques. They pose no additional risk to human health or to the environment. GM crops have many benefits that people overlook; they require fewer chemicals to protect them, like pest-resistant cotton. GM crops can also benefit farmers as they are more reliable and resistant to stress. Some farmers are so eager to use these crops they have had to be pirated in, for example Bt cotton was pirated into India. GM crops are also safer and more precise than mutagenesis techniques.

However, I don’t think that this evidence and these benefits are enough to change the negative opinion that society has on GM crops. I think people need to be shown that scientists, like Doohan, are now producing GM crops for the public’s benefit.  I am of the opinion that we need to change the negative attitude toward GM crops that the big companies have created and, unfortunately, this may take a very long time and a lot of effort in order to convince the consumers. It makes sense that, in order to feed 9.5 billion people on the land area that we have to grow food, with limited water, pesticides and fertilizer, and with the hugely changing climate, we need to be looking at alternative ways for human survival. Maybe GM crops are the answer.

Author: Gina McLoughlin

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Are we just clutching at straws or is there grain of hope in the battle to save our crops from destruction?

Food, we can’t live without it, we can’t live on it if it’s diseased. This is the motivation behind the work of Fiona Doohan and her team in U.C.D, who are striving to improve the security of the world’s food supply by improving the resistance of cereals such as wheat and barley to the many diseases that currently threaten their very existence. During her seminar on Friday the 22nd of November in Trinity’s Botany Lecture theatre, she outlined the main areas on which her work focuses. At the heart of which is research dedicated to plant disease control and stress resistance, as well as the potential influences of climate change and adaptation to disease.

Currently approximately 2332 million tonnes of cereals are used worldwide each year and they are considered to be a universal staple food in the diet of humans, making Fiona’s research all the more important.

During her talk she discussed one of the main diseases of interest to her group, “Fusarium Head Bight Disease” (FHB). This is a fungal disease affecting crops of Wheat and Barley, causing visible bleaching of the infected cereals early after infection.

The real trouble with this fungus however is that it produces a mycotoxin known as deoxynivalenol (DON) which leads to significantly reduced yields of the crop, and importantly can have toxic effects for animals and humans and as such infected crops are not allowed enter the food market, resulting in significant loss to revenue for farmers.

The big problem when attempting to control and prevent FHB is that fungicides have proven to have little effect on controlling it.

One of the big steps forward in tackling this fungus was the discovery of the significance the role of DON plays in spreading and maintaining the infection. Research has shown that if the DON toxin is knocked out early on the infection will be reduced and the bleaching symptoms do not develop. Also, without the DON toxin, there will be no adverse toxic effects for humans and animals thus removing the food safety concern.

Interestingly not all wheat is susceptible to FHB and DON; some exotic wheats are naturally resistant to the toxin and fungal disease. This has led to researchers asking what are the mechanisms and genes that lead to potential resistance to DON/FHB. Using gene expression studies to isolate possible genes associated with DON resistance, Doohan’s team have discovered several genes which they believe to be of interest, most noticeably one particular orphan gene.

Orphan genes are genes which are restricted to a certain lineage. They are particularly important in stress resistance, but are often ignored. It is on the role this orphan gene plays in DON resistance that Doohan’s team have centred their research efforts. Noting the importance not to tissue specificity per say but it’s specificity to DON, the orphan gene will not have an effect on mutant strains of DON. However, when artificially expressed in a non-exotic strain of wheat that would normally express DON when infected, the orphan gene has been shown to inhibit the expression of DON thus inhibiting the development of FHB.

Though these results are very encouraging, the true significance of this discovery and whether it can be applied practically to the production of crops is still waiting to be tested. Unfortunately due to strict European laws the first tests on genetically modified, field planted crops are likely to have to take place in the U.S.A. However Doohan’s research does offer a glimmer of hope in the rather bleak fungus covered problem FHB and it’s (g)rain of terror on stalks of wheat all over Europe.

Author: Joanna Mullen

Image Source: Wikimedia commons