Tag: seminars

Posted on

Seminar series highlights: Nathalie Pettorelli and John Hutchinson

space monitoring

As mentioned previously on the blog, Andrew Jackson and I started a new module this year called “Research Comprehension”. The module revolves around our Evolutionary Biology and Ecology seminar series and the continuous assessment for the module is in the form of blog posts discussing these seminars. We posted a selection of these earlier in the term, but now that the students have had their final degree marks we wanted to post the blogs with the best marks. This means there are more blog posts for some seminars than for others, though we’ve avoided reposting anything we’ve posted previously. We hope you enjoy reading them, and of course congratulations to all the students of the class of 2014! – Natalie

Here’s Sam Preston’s take on Dr. Nathalie Pettorelli’s seminar, “Monitoring biodiversity from space: a wealth of opportunities” and Gina McLoughlin’s views on Professor John Hutchinson‘s seminar, “Six-toed elephants and knobbly-kneed birds! Case studies in the evolution of limb sesamoid bones.”

———————————————————————–

Three New Reasons I Want a Satellite

Sam Preston

Despite the best efforts of Google spying on my house and Lee Tamahori making Die Another Day, I still think satellites are awesome. Who among us can honestly say that man-made objects floating in space aren’t straight up cool? And that’s without even considering what we use them for. Where would we be without the internet, or GPS? Probably outdoors, and lost.
But satellites have utility that extends beyond the realm of kittens in top hats, as Dr. Nathalie Pettorelli from the London Zoological Society knows. She gave a memorable seminar on the use of satellites in biological research, single handedly doubling the number of items on my “Reasons I Want a Satellite” list.

1. Vegetation Surveys
The point of owning a satellite – apart from the prestige and party scene – is being able to do cool stuff with it. Unfortunately, most satellites don’t have the kind of firepower necessary to ransom the Earth, but they do have cameras, and there are a lot of uses for a camera in space. For the botanically-minded, vegetation surveys are one possibility.
Working out what trees and how many are in a particular place can be time consuming. You have to go out, pick survey plots, count and identify trees, often in very remote locations miles from the nearest western toilet. Not when you survey via satellite.
To conduct a satellite survey you simply wait until your satellite is overhead, then take pictures. The scale of these pictures can vary from a few tens of centimetres to metres, and once you have them you’ve saved yourself a lot of time, money, and effort. Then you can use your satellite images to spot illegal logging of rainforest, or examine how storms affect mangroves. Best of all, your camera isn’t restricted to what your eye sees. By examining the relative amounts of red and near infrared light reflected from the Earth’s surface, you can determine the “greenness” of vegetation, assess its seasonality, and judge its composition, all of which is vital for finding habitat for reintroduction programs.

2. Multi-Scale Ecology
Two of the seminars we’ve enjoyed have been about ecological scales. Unfortunately, it’s often difficult to obtain data on the largest scales, so unless you’re willing to put in obscene amounts of work and time, you’re not going to get any meaningful information. That is, unless you have a satellite.
Once again satellites trump doing things by hand. They can survey large areas much more quickly and many times more than even the most dedicated research team, and depending on what you’re looking for can provide highly valuable information. Want to assess eutrophication of freshwater? Check out the “greenness” of the lake’s phytoplankton. Want to determine the clarity of the water? Use lasers emission and work out the absorbance rate. If the phenomenon you want to study affects light absorption or reflection in any way, then satellites should be up to the task.

3. Counting Penguins
By now you’ve noticed the theme of my satellite-based projects. When it involves very large – or just difficult to reach – areas, then you can probably do it faster by satellite. But satellite projects aren’t just limited to plants and ecosystems. They can be just as useful for surveying animals over large, hard to reach areas, and there are few areas as large or hard to reach as Antarctica.
If you’ve ever wondered how many penguins are at the south pole, you’re not the only one. We’ve all pondered the number of well dressed birds that manage to carve out a stylish existence on the ice. One research team, however, decided to do something about it, and – you guessed it – they did it with satellites.
The idea is brilliant in its simplicity: take photos of penguin guano from space. Yes, that’s right: millions of euros of equipment used to photograph poo. From space. That has just the bizarre and disgusting ring to it that marks a good zoological study. Outlandish as it may sound, using this method the team discovered 10 new penguin colonies in Antarctica! What’s more, using satellites operating at a finer scale, other researchers were even able to estimate the sizes of penguin colonies!
To sum up, satellites and biological research go hand in hand. No longer is space the privileged realm of the physicist looking down on the (erroneously) perceived softer scientists. Zoologists, botanists, and ecologists have carved out a territory in orbit. There are a lot of questions we’ve yet to face, but the answers are out there.

—————————————————————————–

Walking on Tenderfoot

Gina McLoughlin

Being an avid follower of a blog called What’s in John’s Freezer naturally I was extremely excited when Professor John Hutchinson from the Royal Veterinary College, London came to give us a seminar. He gave a very interesting and entertaining talk on 6-toed elephants and knobbly-kneed birds: Case studies in the evolution of limb sesamoid bones. Hutchinson explained to us about his recent research into the tiny sesamoid bones, such as the patella, that are found in the limbs of many animals. Sesamoid bones are small “bits” of bone that are generally located in a tendon or near a joint (Sarin et. al., 1999). Their function is not fully understood but it is hypothesized that they may play a role in changing the direction of muscle forces in a limb or may play a role in protecting the tendons.

A very interesting case of such sesamoid bones, which Hutchinson talked about, is found in elephant feet. Elephants, like humans have 5 toes but unlike humans they stand on their tiptoes and have a hoof-like sole. They have a fat pad at the heel of their foot, which acts as a cushion and supports the toes. It is here, buried deep in the fat tissue that the pre-digit bones are found. Hutchinson explained they are like a 6th toe that can be found in both the front and the back feet. The bones are known as the prepollux and prehallux and they connect to the real toes just under where our thumb is (Hutchinson et. al., 2011). They are cartilaginous for most of the elephant’s life, but do eventually ossify when the elephant gets older. Again, the function of these sesamoid bones in the elephant is not fully understood although Hutchinson proposed they could be used as levers for extra support due to the weight of the elephants. Another hypothesis is that instead of developing a single hoof, like in a horse, the elephants use this pre-digit to distribute their weight more evenly on each foot (Hutchinson et. al., 2011). However, these pre-digits have been observed in other animals and have different functions than what they have in the elephant. Most surprisingly to me was that they are found in pandas. Here, they are used for grasping bamboos while eating, kind of like a false thumb. Their 5 fingers close over the false thumb, which has evolved by enlarging the radial sesamoid and functions as an opposable thumb (Endo et. al., 1999).

A thought provoking point that Hutchinson made in his seminar was how do such small bones cause big problems in animals. These bones can cause such big problems that it almost makes big animals appear very fragile. For example, elephants in zoo need to have their feet very well looked after to prevent them from going lame. Hutchinson explained that if an elephant goes lame due to a sesamoid bone problem it is more than likely that the elephant will be dead in approximately 5 years time, as it is very hard to fix and they are in a lot of pain. Likewise, giraffes need a lot of hoof-care to prevent their sesamoid bones from dissolving completely. This would cause the giraffe to go lame and prevent them from thriving.

A more common animal example of a sesamoid injury that I find very interesting, and an area where more research needs to be carried out, is in horses. The sesamoid bones from which most injuries occur are located in the lower limb, at the back of the fetlock joints in the both the fore and hind limbs (Figure 1). In horses it is hypothesized that these bones are used as a pulley for the suspensory ligament as it passes over the back of the fetlock joint. They are very important in the mechanical functioning of the fetlock joint. Horses in competitive sports, such as show jumping and racing frequently suffer from sesamoiditis (Spike-Pierce & Bramlage, 2003). This is commonly caused by heavy loading on the limbs and over-flexion of the fetlock joint, which can result in the sesamoid ligament tearing. This extra pressure can lead to increased internal bone stress, which may lead to a fracture of the sesamoid bones. Faulty blood flow to the bone can be a result of this damage and demineralization of the bone can occur.

Figure 1: Labeled diagram of an equine lower limb showing the fetlock joint and sesmoid bones.
Figure 1: Labeled diagram of an equine lower limb showing the fetlock joint and sesmoid bones.

Thankfully, most cases of sesamoiditis can be treated with anti-inflammatory medicine, cold therapy and support strapping or bandaging. However, in more serious cases where a fracture has occurred the horse may never return to the top of their sport due to the damage (Kamm et. al., 2011). Once a sesamoid bone is damaged they are very difficult to cure because every time the animal walks they put more pressure on the bone, preventing it from healing.

By the end of the seminar I was amazed that such small bones could be so interesting. I would never have though that these tiny bones could be the cause of such big problems not only in competitive horses, but also in large animals such as elephants. Overall, I really enjoyed Hutchinson’s talk. I thought he was a very good speaker and I would now possibly consider doing some research in this area myself.

 

Posted on

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

——————————————————-

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

 

Posted on

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

———————————————————————————

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

Posted on

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

———————————————————————————

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/

Posted on

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

————————————————————–

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

Posted on

Seminar series: Tom Ezard, University of Southampton

Forams

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 Sarah Byrne and Sean Meehan on Tom Ezard’s seminar, Birth, death and macroevolutionary consequences.

Splitting Hares – easier said than done?

In a recent talk given by Tom Ezard, a research fellow and evolutionary ecologist, the definition of a species was examined and challenged. While defining a species may seem a simple task for just about anybody and in particular a room full of people with a biology background, the actual definition can be harder to understand when thinking about fossil or species’ records and gaps across time. Ezard highlights that a dynamic approach is needed when discussing speciation and the definition of a species. Claiming that you shouldn’t define a species at one particular moment in time, he details that large gaps in the fossil record make it very difficult to have a fully complete picture about speciation events. In other words, making inferences about speciation events from a certain snapshot in time could overlook the dynamic process of change that occurs over time and give us inaccurate theories about the macroevolution of species.

Following on from the definition of a species, Ezard was interested in the fossil record and how it can give us information about the species record and also, more importantly, about diversity. He was interested in finding out where these gaps in the fossil record had occurred and what impacts they could possibly have. In graphs he provided, it was clear that there was a difference between data over time with more species surges found in recent data in comparison with the past, indicating the number of species has increased over time. However, it’s a little misleading because as time develops we learn more about how to indentify species of have better techniques to do so, it is therefore unclear as to whether or not there has been a big increase in species.

To better explain some complicated parts of the speciation theory, Ezard used a baseball analogy which I was thankful for, showing a picture of various baseballs over time. Ezard explained how techniques improve over time and how the original was very different to the new and modern ball. All of the baseballs of various different ages, textures and shapes remained part of one game (or one species) and that there was no split into a new game (or new species). He stressed that this continuation was very important in understanding macroevolution and when identifying species, that it was vital to look at gaps in the lineage. This brings us back to the fact that the fossil record needs to be examined further and the question of what is meant by a species may need to be redefined. Ezards definition of a species as ‘a single line of descent, a sequence of populations evolving separately from others seems closer to the real definition than previously thought.

Speciation was also a key factor of Ezard’s talk and he was interested in identifying budding speciation events while still being able to identify their ancestors. Two main types of speciation and evolution were discussed in the talk, one type; anagenesis refers to a change along a branch of a phylogeny or the evolution of a gradual change within a species over time. This theory was backed by Darwin and eventually leads to a speciation event. In contrast, cladogenesis, where a population stays stable until a big speciation event happens suddenly and then a splitting occurs between species that ensures they can then not reproduce with each other.

The split can be caused by either biotic or abiotic factors with disagreements regularly occurring between geologists and modern evolutionary biologists over whether the biotic factors (such as competition) or the abiotic factors (such as climate) are the main key drivers affecting species ecology and diversification. So, what is the main driver affecting species ecology and in turn speciation and diversification? Ezard was interested in finding this out.

Using observational studies, algorithmic processes and a multivariate complex approach, Ezard was able to account for ecological differences between species. Lotka’s equation gave an estimate of birth and death models that detailed speciation probability and extinction risk. Species respond differently to global drivers of change and these differences have macroevolutionary consequences. The Red Queen Hypothesis mentioned above, a biotic factor that describes how predator and prey are continually adapting to out-do each other affects species much more so than climate does, and in comparison, climate, an abiotic factor has much more of an effect on extinction.

So, it seems that a combination of both factors are important although they affect both speciation and extinction at different rates. Ezard indicated that, in order to understand diversity, it was first necessary to understand the biotic factors that impact the split and to then devise a model to draw these two areas together. Ezard’s enthusiastic and engaging approach clearly showed his passion for the subject and the interesting topic left me with a lot to think about it.

Author: Sarah Byrne

——————————————————————-

Lumpers and Splitters: Apparently they’re not varieties of potato

What is a species? This question seems so fundamental to biology that surely the experts have answered it by now, right? Wrong. Defining a species is a difficult thing, and each new definition seems to come up short in certain criteria. For example Ernst Mayr’s widely used definition of a species: “groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups” completely disregards species which reproduce asexually. For this reason I like Simpson’s evolutionary concept for defining a species and this is precisely what Tom Ezard uses for his work on macroevolutionary dynamics. This concept holds that each species represents a single line of descent; it begins with a speciation event and terminates with extinction. Ezard used the evolution of the baseball to demonstrate this concept. Although the modern baseball is considerably different from its original ancestor, it is still a baseball and there have been no ‘speciation’ events or splits in the lineage to form a new type of ball.

It was Darwin who first coined the term ‘lumpers and splitters’. Lumpers are those biologists who tend to ‘lump’ many ‘species’ in together as one. The splitters are those biologists who like to make as many ‘species’ as possible. In his 1945 work ‘The Principles of Classification and a Classification of Mammals’ George G. Simpson notes rather sardonically: “splitters make very small units – their critics say that if they can tell two animals apart, they place them in different genera … and if they cannot tell them apart, they place them in different species. … Lumpers make large units – their critics say that if a carnivore is neither a dog nor a bear, they call it a cat.” So we can see that this problem is an old one, and that Simpson’s evolutionary concept is very useful for defining species in macroevolutionary studies.

In order to study macroevolutionary dynamics one needs a fairly detailed picture of a clade’s development, and not many organisms provide a suitable fossil record for a detailed study. Fortunately Ezard and his team found the perfect organisms for this purpose; the Foraminifera. These creatures are marine dwelling amoeboid protists. When they die they sink to the bottom and leave behind their calcium shells or tests. They are deposited and preserved on the sea floor and in the right conditions over time can form stratified layers of fossils which give a very complete picture of their evolution over time. Also,the stable isotope ratios of oxygen in the shells can be used to reconstruct palaeo-climatic conditions. These attributes make them incredibly useful in the study of macroevolutionary dynamics.

So, what are the driving forces of speciation? Is there one factor which influences this process above all the others? This is what Ezard and his team set out to investigate. The foraminifera had an interesting story to tell. It was found that incipient species diversify the fastest. This was found to be primarily due to biotic factors or ‘Red Queen’ factors. As a clade grows older it was found that diversification slows due to diversity dependence. However, it was found that extinction is primarily influenced by climatic or Court Jester factors. These findings are important in order to grasp a general understanding of macroevolutionary dynamics. It means that impacts of diversity and climatic fluctuations are not felt uniformly across a phylogeny.  More simply put, it means that the extent of the effect of biotic and abiotic factors on a clade depend on how old it is.

In summary, what Ezard and his team found was that there is no dominant macroevolutionary force, but that, a combination of biotic and abiotic variables drive speciation and extinction. They also found that species’ ecologies are important driving forces in these processes.

Author: Sean Meehan

Image Source: Wikicommons

Posted on

A Year at EcoEvo@TCD

Trinity 3D NYE 2

The Christmas decorations have been banished for another year, stashes of left-over turkey are dwindling and the hollow echo of empty biscuit boxes tone the end of holiday indulgences. As the promise of ever-longer evenings beckons and the first, brave (or fool hardy) snowdrops contemplate their next move it’s that time for the inevitable “year in review”. Rather than a countdown of favourite scientific discoveries from the year, I thought I’d celebrate a year in the life of EcoEvo@TCD.

We dusted off our competitive spirits in January to open the year with a month of blog games. Apocalypse Meow trashed the competition to win the prize for most hits for a blog post in a single day thanks to a winning formula of cute cats, birds and reddit. The cuteness theme continued with insights into why we often experience mildly violent and destructive reactions to coping with cuteness.

We’re lucky in Dublin to receive annual visits from Brent Geese, the beautiful transatlantic migrants who enliven many a winter walk. The birds were the subject of some controversy in March with a somewhat unlikely foe. The researchers who follow the geese are no less interesting and were kind enough to take some of the EvoEvo@TCD team under their wing…

We’re a diverse bunch. Our research interests lend themselves to trips to beautiful natural history museums and the opportunity to poke through some museum treasures.On the lab and field work side, we work with bees, vultures, Indonesian birds, badgers  and sometimes the animals even visit us (it’s not all just about computers…). Our School of Natural Sciences postgrad symposium in April showcased the diversity and quality of current research in our School.

Some of our more popular posts are advice pieces on how to survive and thrive in academia. From how to retain your sanity during long lab experiments to thesis writing, how to find a PhD and why you should consider coming to work with us in particular, EcoEvo@TCD is your one stop shop on how to survive as a student.

And we don’t just have tips for students. Most of the EcoEvo@TCD team are active on twitter and I think we would all agree that twitter is a great resource for academics of all levels with far more benefits than downsides. Armed with science networking tips, we set forth into a summer of conference season madness. Our ranks were divided as we attended different conferences, the main ones being INTECOL in London and ESEB in Lisbon.

Many of our advice and perspective pieces arose from our weekly NERD club meetings where we bashed out the details of our current projects, prepared for conferences and seminar presentations and  benefited from academic survival tips and collaborated within group projects. All of which culminated in our all-important NERD club AGM.

We had multiple forays into the world of science communication and outreach. We gave guided tours of the Zoology department’s museum over the summer and recounted the exotic tales of some of our animal residents. The museum opened its doors to the public for free as part of Discover Research Night when we showcased some of our department’s current research. Media and blogosphere reactions to some of our publications were interesting to say the least. From dealing with creationist backlash to negotiating the media storm surrounding a paper that went viral, even when that media attention is sometimes off the mark, we’re a far more media savvy bunch than before.

This year is all set for more EcoEvo@TCD fun. In February we will have our postgrad symposium and we welcome a new Chair of Zoology to the department. Our Friday seminar series continues this term so expect more insights from our final-year undergraduates. There will be more articles arising from our NERD club discussions, conferences galore in the summer as well as research and fieldwork tales.

Happy New Year EcoEvo@TCD!

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

Image Credit: www.joe.ie

Posted on

Seminar series: David Angeler, Swedish University of Agricultural Sciences

FoodWeb

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 Somantha Killion-Connolly and Joe Bliss on David Angeler’s seminar, Ecological complexity: a torture or nurture for management and conservation?

Panarchy – Sense or nonsense?

Scientists have been told for many years now to lift their heads from their microscopes, look up and take in the bigger picture. Well the picture has gotten even bigger and more complex according to the hypothesis of panarchy (Gunderson & Holling, 2002). In a recent seminar by Dr. David Angeler of the Swedish University of Agricultural Sciences, Dr. Angeler attempted to communicate this approach as the way forward in ecosystem management. If you were to do a search of the internet for the definition of panarchy, don’t expect a nice simple concise definition, as this controversial approach takes a bit of explanation. Ecologists have been providing evidence for decades showing that ecological systems are far more complex than imagined. Panarchy attempts to provide a conceptual framework for characterising the interactions between ecological and human systems in order to manage them in a sustainable manner.

Panarchy seeks to find common ground between economic, social and ecological theories. This seems like a big ask and paradoxically the way it seeks to achieve this is, using Dr. Angeler’s analogy, to break up the big picture into smaller pieces to make a jigsaw puzzle. Where the hypothesis begins to make a lot of sense is that is requires you to take not only a top –down, as was traditionally used, but a bottom up approach also. Ecologists have traditionally investigated ecological communities and how they have changed spatially and temporally. Dr. Angeler proposes to instead look the big ecological picture in terms of scales. We should not only be looking at how organisms at different scales are affected by biotic and abiotic variables in time and space, but also the interactions between scales. Therefore, according to panarchy, ecological systems consist of scale specific structures and processes that change and interact as you advance through the scales. The further spatial dimensions are increased, the slower the processes are in the environment and vice versa.

Where the theory begins to get more complicated is when you need to view an ecosystem and its constituents as undergoing a continuous cycle of change, with four defined stages. The stages are referred to as the exploitation stage (rapid expansion in an open niche), conservation stage (accumulation of energy and a period of stability where the carrying capacity is reached), the release stage (period of rapid decline due to changes in pressures) and the re-organisation stage (period of natural selection from the pressures of the release stage).

Dr. Angeler in his research on the invertebrates in freshwater lakes of Sweden (Angeler et al., 2013) has shown how the theory is empirically testable using multivariate time series modelling. This method is based on a redundancy analysis and adapts a spatial method to time series analysis. Using this long term data set collected by his University, Angeler’s aim was to track changes in the species community and gain an understanding into what are the vulnerabilities of these vertebrate communities to changes in their environment.  The practical goal of this work is to prevent a system from reaching its tipping point. The results of this study suggested that studying processes that happen on a temporal scale which are un-related to general environmental changes has strong management and conservational potential. Personally, I think the main concepts of panarchy do make sense but its application and the analysis required is far from simple and it really is a difficult idea to communicate.

Author: Somantha Killion-Connolly

—————————————————————————-

Multivariate Time Series Modelling Explained
I think the language of science often hinders the communication of ideas and restricts them to a narrow audience of specialists. I attended a talk given David G. Angeler presenting his research on Ecological Complexity using Multivariate Time Series Modelling and the Panarchy concept to study the condition of a number of Swedish lakes. I found it difficult to even understand what the research was about so, I have been inspired to write this blog and explain part of this complex topic, in simple language which I hope will be graspable for a wider scientific audience.

Let us start be first breaking down the term “multivariate time series modelling” and studying its parts.  Multivariate means more than two variable quantities. In this context of studying ecological complexity, these variable quantities include the number of organisms of a particular species or species group as well as abiotic factors such as mineral concentrations and water temperature. Time series modelling involves plotting data at uniformly spaced time intervals.  So multivariate time series modelling is plotting multiple variables against time.

The benefit of plotting multiple variables such as multiple abiotic factors and a species population’s numbers on a specific time scale is that it allows you to find correlations between factors. For example, if we take the population numbers of a plankton species which were sampled once a month in a lake we can plot the population number over a year and see how the population fluctuates. Our plankton may show fluctuations up and down over the year. To investigate whether any of the abiotic factors influenced the fluctuations in our plankton numbers we can plot how the abiotic factors fluctuated over the same time span and see if any of them correlate with the fluctuations of the plankton. If any of the abiotic factors fluctuate with the same rhythm as the population then we might suspect this in an important factor influencing the population. However this doesn’t rule out the possibility that the abiotic factor itself varies with the population number but is not the cause of the fluctuation, correlation does not prove causation, but this can then be investigated by experimentation.

Another important benefit of using multivariate time series modelling, which Angeler used when studying the ecology of his lake, is that it allows us to see correlation at different time scales. For example plankton may fluctuate up and down in a regular pattern in response to annual variation in day length. But on a longer time scale, say over 20 years, there may be a trend of increasing population numbers due to a large scale effect such as climate change.

Looking at ecological variation using multivariate time series modelling allows us to assess how organisms are responding to different conditions on small and large time scales. Angeler hopes to use these data to assess the health of ecosystems and to understand how they will be able to handle changing conditions such a global warming. He suggests that management may be able to aid ecosystems facing this large scale change by affecting them in ways which act on smaller scales.

Author: Joe Bliss

Image Source: Wikicommons

Posted on

Seminar series; James McInerney, NUI Maynooth

McInerney

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 Dermot McMorrough and Maura Judge on James McInerney’s seminar, The hybrid nature of eukaryotes rejects the three-domains hypothesis of life on Earth.

Time to stop the press? Science for the Masses.

What exactly constitutes “pop science”? What is it that takes a piece of research from the relative anonymity of peer-reviewed journals and academic conferences to mainstream media outlets and the masses?

Dr James McInerney addressed a topic of monumental importance to the way we understand life on Earth. If his findings are accepted and withstand the test of time, we will actually have to rewrite biology textbooks around the world and that’s a pretty big deal. I must admit I was impressed with his claims, and he seemed incredibly thorough with how he went about proving them. At the end of his impressively complex and graphic filled presentation, I was left with one main question: why was I only hearing this now? His paper has been accepted by the Proceedings of the National Academy of Sciences (impact factor of 9.737), and has implications for almost every field of biology, so why isn’t this being shouted from the rooftops? My inner nerd wants answers and is feeling quite indignant at this stage.

After some thought and discussion, I think I’ve found my answer: People don’t care. My inner nerd has retired to the bar; it’s a harsh reality to take.
I was once told that information, not money, makes the world go around. While this is a romantic notion for someone fascinated by learning new things, that information is rarely free.

Science is often reported in mainstream media. People like to think they’re learning something new on their way to work, and so stories with a scientific undertone (and rarely more) are common in daily newspapers and in the general media pick and mix. These articles often do have scientific background, but have been so bastardised to make them more digestible that they are scantly recognisable as related to the original research. Recently, here in the department of Zoology, many of us were surprised to hear that our own Kevin Healy and Dr Andrew Jackson had become “fly experts” according to media outlets such as Today FM. How do you make the move from macroevolution and computer modelling to entomology and pest control overnight? You don’t. The media does that bit for you. The story needs to be easy to understand, and while the flicker fusion rate study was fascinating, it can be hard to grasp if you’re not familiar with the background. I’m not exactly happy with how this happens, but if it gets the scientists (who’s work so often goes unnoticed by the public) a bit of publicity, then it’s a price I think we’ll have to be willing to pay. Science is not immune to the realities of economics and so needs funding to survive. If a story about flies helps them get a grant to further their research in a field completely unrelated to entomology, so be it.

What has this got to do with the seminar? Dr McInerney just rewrote the book on the domains of life, not a species or a phylogeny or insects – the domains of life! Surely the people would want to know this right?
Science editors in news outlets will “dumb down” these stories as not to make their audience feel inadequate (who reads a newspaper to feel stupid?). The problem with the domains of life story is that dumbing it down could take a while – a long while. I’ve done 3 years of science, one of which supposedly specialises in this field and it took me a while and a lot of help to figure out how he was going about proving his claim. To get that story onto the front page of the Herald, you’re going to have to write very small and hope the average reader has a clue what a domain even is.

So can this story ever make it to the masses? It’s not going to be easy. For science to make the headlines, it usually has to involve the word cancer, obesity or global warming – either with the intention of condemning us for being fat, lazy death traps, or better still telling us we can cheat death a bit, while still being fat lazy death traps.

I was impressed with Dr McInerney’s talk, at least what I understood of it. I do, however, have one caveat before this is unleashed on the world. To change dogma such as the current domain hypothesis, you need to be able to explain it more or less in one sentence. People do not accept change like this lightly. I got the impression he struggled to get his explanation into a one-hour slot in a room full of undergrads and academics. If he can explain it in simple terms, he’s onto something. My inner nerd has hope yet.

Author:Dermott McMorrough

———————————————————————-

The seekers of truth?

As Richard Dawkins says in the selfish gene “those who choose to study it [Zoology] often make their decision without appreciating its profound philosophical significance”. I personally feel this statement could not be truer. After a debate regarding evolution the other week, a fellow classmate remarked “I just don’t like thinking about all those deeper questions”. Is this the right attitude? Einstein did not believe so. “When I think about the ablest students whom I have encountered in my teaching, that is, those who distinguish themselves by their independence of judgment and not merely their quick-wittedness, I can affirm that they had a vigorous interest in epistemology (branch of philosophy that studies knowledge)” (Einstein 1916).

In a seminar delivered by Professor James McInerney he asked the question of how complex life really began. He began his talk by highlighting the importance of philosophy and of past philosophers in his work. This idea intrigued me and I began to ask, are we neglecting this important link? Karl Popper, a German philosopher, wrote many books in the 1960s electrifying the scientific community. He said you are doing science if you can invent an experiment that proves yourself wrong. This idea is known as falsifiability and is sometimes synonymous to testability. As you can see, this idea of proposing and testing hypotheses in a way that allows you to reject them is in keeping with the modern day, highly relied upon, scientific method. Popper stressed the problem of demarcation, which is distinguishing science from non-science or pseudoscience and made falsifiability the demarcation criterion. This means that what is unfalsifiable is classified as unscientific. However there is a problem with this; evolutionary scientists cannot falsify their observations and hence even the theory of evolution is still only deemed a theory. Popper later amended this, saying you definitely know you’re doing science if can you can falsify your experiment but some things fall outside this possibility such as the theory of evolution where the event has already happened and you cannot replicate it in the laboratory.

William Whewell, a British philosopher from the mid 19th century, who originally coined the term scientist (originally referred to as a natural philosopher) then coined the term consilience. Consilience means the convergence of evidence. It’s the principle that, if evidence from multiple independent, unrelated sources are in agreement, you can draw very strong conclusions even if the individual sources of evidence are not strong on their own. This is the case for the theory of evolution as independent data sets from various field such as genetics, chemistry and physics back one another up, agreeing with the mutability of species over time. Hence induction is consistent and evolution is thought of as a strong idea. Today, McInerney uses this idea in determining the origin of Eukaryotic cells, finding strong supporting evidence for a single hybridization event resulting in a single domain of life, as opposed to the three domain hypothesis.

Hence science is indeed founded by philosophers and we are the modern day “natural philosophers”. Science was originally constrained by religion, e.g. Charles Darwin’s struggle in the publication of the theory of evolution, due to the non-religious inference that humans are indeed animals. Thanks to philosophers such as Popper and Whewell we can disregard non-science and hence have come a long way since the idea of “the ladder of life” with God and angels positioned at the top rungs, then royalty, humans below, and finally animals. However we don’t often think about the philosophy of science and evolution. When I told my elder cousin that I was interested in evolutionary biology her response was “Evolution…sure isn’t that figured out?”. Before, we were restrained from addressing philosophical questions by religion, now it seems we have become absorbed in the facts and statistical data with a disregard for the broader questions that science and philosophers set forward to address. Nowadays, if you don’t adhere to popular scientific dogma, your theories easily face rejection. The majority of scientists are evaluators of data and not pioneers, creating original ideas. However, only those with a talent for original thought can be pioneers such as James McInerney who combats the commonly held belief of the three domains of life. Science is the tool to answer philosophical questions and we cannot ignore our ancestors, the philosophers, who gave birth to us scientists.

As Einstein said, in response to a physics lecturer’s proposal to  introduce as much as possible of the philosophy of science into the modern physics course, “independence created by philosophical insight is, in my opinion, the mark of distinction between a mere artisan or specialist and a real seeker after truth.” (Einstein, Dec 1944)

Let us not seek only money and acceptance, let us become the seekers of truth.

Author: Maura Judge

Image Source: Wikicommons

Posted on

Seminar series; Britt Koskella, University of Exeter

HorseChestnut

The first set of our weekly Wednesday posts by final-year undergraduate students as part of 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 Sam Preston and Emma Dunne on Britt Koskella’s seminar, Bacteria-phage interactions within their long-lived hosts

Evolution Gone Viral

Forget Darwin’s finches and forget the cichlids of Lake Malawi. if you want to see natural selection and evolution in action you’re going to need to think a lot smaller, because evolutionary biology’s gone viral.

One of the problems with adaptive evolution is that it happens on a scale we can’t appreciate. Generations of human lives can come and go and natural selection’s hardly gotten started. For the most part we’re stuck observing current diversity – the results of past natural selection – and interpreting it as best we can to get an idea of the evolutionary processes that shaped the organisms we see today. But that’s not the case with phages.

Phages – short for bacteriophages – are viruses that infect bacterial cells. They can produce thousands, even millions of copies of themselves in a matter of minutes. Each bacterial cell lysed by a phage represents a new generation of virus particles produced in less time than it takes to make a cup of tea. Every new generation is an opportunity for natural selection to go to work, and evolutionary change that might take thousands of years with larger organisms occurs in a matter of days with phages. This makes them almost perfect organisms for evolutionary study, an idea that is by no means novel; phage evolution has been studied intensively by biologists attempting to account for the origins of these ubiquitous organisms and the mechanisms of their gene transfer.

Britt Koskella and a handful of other researchers, however, are taking the study of phage evolution to new places. It is already known that the rate at which parasites adapt to their hosts has an impact on the host community structure, and there’s little that can adapt as quickly as a phage. Koskella’s research aims to determine how phages, by coevolving with their bacterial hosts, can influence the community structure of higher organisms.

Bleeding canker disease is a problem for horse chestnut trees (Aesculus hippocastanum) in the UK. It’s caused by the bacterium Pseudomonas syringae, which is itself parasitized by phages found in and on the leaves of A. hippocastanum. This is the model Koskella uses to explore phage adaptation to overcome bacterial resistance. In an elegant experiment, she showed that phages become locally adapted to P. syringae in the same tree (i.e. phages of a given tree are more infectious to P. syringae from the same tree than another).

In another experiment Koskella showed that this adaptation is met with counter-adaptation from the bacteria. By freezing phage/bacterium samples taken at various times in the year, she was able to test how resistant bacteria are to phages from the same time period, from earlier periods, and later ones. She discovered that bacteria from either the same or slightly earlier time periods relative to the phage were most susceptible to infection, whereas bacteria from later time periods were less susceptible. Interestingly, bacteria from much earlier time periods relative to the phage were also less susceptible to infection than contemporary bacteria. This result is particularly interesting, as it undermines the prevailing “evolutionary arms race” hypothesis of competition-based coevolution, instead suggesting that adaptations, when acquired, incur costs such that when they are no longer useful (i.e. when the phage/bacterium has adapted to cope with them) they are selected against and lost from the population.

The decision to investigate these evolutionary processes using P. syringae is an important one. By illustrating how phages affect a serious, disease-causing bacterium Koskella highlights the potential for phage adaptation to have a dramatic effect on tree communities. And if phages play a role in determining the structure of communities of primary producers, then one might expect knock on effects on the rest of the food web.

I think it’s fair to say that Koskella’s field of research is still in its infancy, but the premise is exciting nonetheless. For myself, there are a lot of unanswered questions that future research might address. To what extent do phages actually benefit the plants they’re in? Is there a cost to trees for harbouring phages? Can plants and phages coevolve, perhaps with plants encouraging phage residence to act as a symbiotic immune system?

Phages are already beginning to see use in biocontrol in American agriculture, but our knowledge of their function in the environment is only rudimentary. There is a great need for more research on their role in shaping the evolution of communities. If our irresponsible use of insecticides in the 20th century has taught us anything, we want to know everything we can about phage interactions before we cause irreparable harm.

Author:  Sam Preston

————————————————————————————

Superbugs’ Kryptonite

Antibiotics have long been hailed as one of the greatest scientific achievements of the twentieth century. These little miracles were once doled out in their multitudes to do battle with our ear infections, kidney infections, throat infections, sexually transmitted infections and all-colours-of-nasty infections. But has the situation turned full circle, are we reverting back to a world “pre-antibiotics”?

Superbugs and their vigorous resistance to antibiotics are presently charging through the media. Our abuse of antibiotics has rendered them useless against such a massive force as a rapidly evolving bacterial infection. Don’t we all know at least one person with a stash of AugmentinTM in the back of their medicine cupboards just in case they catch a cold? One can only cringe while pondering on how they managed to build such a stash. Using antibiotics as a stronger version of over the counter medicines is a worryingly fashionable form of personal healthcare. It has led to many strains of bacteria becoming completely resistant to their former attackers.

But don’t hold up your white flag in surrender just yet. Bacteriophages are marching into the mainstream as the new superheroes. As the Greek origin of their name suggests, these viruses “devour” bacteria and then replicate within them. Described as “viruses that cure” by the BBC in an informative documentary on their history, bacteriophages have been used as an alternative to antibiotics for nearly a century. They once had widespread use, even being used to treat the Red Army in the 1920s. But, they were soon overtaken by antibiotics which were cheaper to make, and easier to prescribe, use and store. The first publications on Phage Therapy (using bacteriophages as treatment for bacterial infections), were mainly written in Russian or Georgian, making them largely inaccessible to the wider scientific community – a community dominated by English speakers still to this day. Phage Therapy has only been formally approved as a treatment for humans in Russia and Georgia, although phages for killing bacteria responsible for food poisoning, such as Listeria, are now in use in the West. Nevertheless, phage treatment offers a compelling solution to superbugs.

Just like bacteria can evolve resistance; bacteriophages can evolve to overcome this resistance. Britt Koskella from the University of Exeter is studying the apparent co-evolutionary arms-race between phages and their bacterial hosts. The results of her 2011 paper on how bacteria-phage interactions shape host populations have important implications for therapeutic phage epidemiology. With phages playing the game bacteria really don’t have a chance. Once the bacteria move the goalposts, the bacteriophages have the ability to change tactics and score. This attribute is making Phage Therapy an attractive alternative to antibiotics.

The list of advantages of phages over antibiotics does not end with their cunning ability to co-evolve with their bacterial hosts. Due to their specificity, they do not affect the useful bacteria lurking in your body and cause malicious side effects. Antibiotics are infamous for causing rashes, headaches, nausea, and diarrhoea – who wouldn’t prefer these symptoms to be eliminated from their recovery? Phages also occur naturally. We ingest numerous bacteria-eaters every day; they do not cause us any harm as they are passing through. They can even be genetically modified to reinforce their fighting power.

Study into the potential of bacteriophages to treat bacterial infections largely ceased when antibiotics emerged. Now that we seem to be reverting to a world “pre-antibiotics” there seems to be space for a revival in these studies. Phages have not-so-recently been used to combat MRSA, a superbug that increasingly plagues hospitals. Research into this is being carried out in Warsaw, a far stretch from the claimed centre of modern medicine. Highlighting the problems associated with the abuse of antibiotics seems to be falling on deaf ears, especially since the stashes of AugmentinTM are only getting larger. Will bacteriophages be allowed to step up and be the kryptonite that defeats the superbugs?

Author: Emma Dunne

Image Source: Wikicommons