Author: EcoEvo@TCD

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Search and rescue or seek and destroy?

military

Curing cancer, delivering carbon free energy and rescuing people trapped after earthquakes are noble pursuits. In a time where fundamental research is under pressure to deliver, lofty goals like this are glibly trotted out in grant applications to justify project funding, and then again in press releases once the work is done to justify the next grant application. I’m throwing stones, but am very conscious that I am not without sin and nor am I living far from my glass house.

While basic research, even apparently far removed from product or cure, undeniably adds to our knowledge base and improves society in unpredictable ways, there is one line of research that warrants extra scrutiny – the military.

Getting funding to do your basic research is ever more difficult in struggling national economies. It can be tempting to get into bed with allsorts, but one has to consider the ethics of taking money from certain sources. I have recently been drawn to the John Templeton Foundation who fund a lot of my kind of research, but some digging has put me off – their founder was, and now his son is, involved in conservative right wing lobbying in the USA. Whatever about the unease of taking money from evolution denialists to get the research done, taking money from the military brings a whole lot more pressing and worrying complications.

By far and away one of the coolest bits of engineering with a biological twist I have ever seen are swarms of flying robots – in particular these examples from the GRASP lab at University of Pennsylvannia. Truly amazing. A marriage of collective behaviour and gizmos made in heaven.

My problem is that many people working in this field gleefully sell us the “search and rescue” potential of these automous swarm. These robots will move about complex environments, scanning and evaluating it like a swarm of foraging ants and locate people trapped under rubble. All well and good, but many of these groups are funded by the military – in the case of GRASP they list projects with input from DARPA and Army Research Laboratories (ARL).

For every innocent engineer in a university playing with cool quadcopters and getting them to play the James Bond theme song, there is a bunch of engineers in military research labs dreaming up new ways to kill people with them. These militarists are smart people: clever scientists, genius engineers and expert in warfare. Their goals are clear – military superiority in the case of DARPA and enablement of “full-spectrum operations” for ARL. Although they all skirt around the issue, this means one thing above all – being able to kill more of your enemy than they can of you.

If killing was my business, I know what I would be doing with swarms of potentially autonomous robots – seek and destroy on unprecedented scales of efficiency. Hordes of flying bombs with redundancy inherent in the system. Lose one and it doesn’t matter, there are thousands following in its wake. Interaction rules that result in network structures that optimise spacing between robots bombs to wreak maximum damage. No more single predator drones patrolling the mountains of southern asia, but swarms of the damn things.

Sometimes the clue is in the name: “grenade camera” leaves little to the imagination. Here’s a trite justification for this 3d camera in a ball – “It is thought the new technology would enable soldiers to see into potential danger spots without putting themselves at risk of ambush”. Obviously protecting your own soldiers is important, but the reality of war is you would drop one of these cutely dubbed “I-balls” around the corner, calculate the proportion of children to combatants in the room and hit the “go boom” button if you were satisfied with the odds.

Behind the games set up in which technologists pit their creations against each other in an action packed fun day out, lies a whole raft of people whose job it is to turn these toys into weapons.
Running,
On our way
Hiding,
You will pay
Dying,
One thousand deaths
Searching…
Search and Rescue
Seek and Destroy

–        Seek and Destroy by Metallica from their debut album Kill ‘Em All.

Author: Andrew Jackson, a.jackson[at]tcd.ie, @yodacomplex

Image Source: Wikicommons

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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

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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

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People are idiots

Elk5

Apologies in advance for this perhaps unconstructive rant! But I’ve found the process cathartic after spending my whole holiday worrying that someone nearby was going to get kicked, crushed or eaten through their own stupidity!

For my summer holiday this year I spent a week in Yellowstone National Park in the USA. It was awesome apart from one thing: the people.

Everywhere you go in Yellowstone and the surrounding areas (including a brilliant sign showing you how to bear-proof your bird feeder in the bathrooms of a BBQ joint in Jacksons Hole) you find warnings about bears. These warnings exist because bears can be extremely dangerous. Male grizzly bears, which are common in Yellowstone, can weigh up to 360 kg and their bite could crush a bowling ball. Not something you want to mess with at close hand! Both male and female grizzlies can also be extremely aggressive when defending their young or a food supply, or if they are surprised and feel threatened.  [If you’re still not convinced that you should be wary of bears I suggest watching the excellent and disturbing documentary “Grizzly Man”]. The warnings remind visitors to keep all their food and scented items (including toiletries) contained at all times, to make a noise on hiking trails to make bears aware of your presence, and to always stay at least 100 feet from a bear. These warnings are not only so the park can avoid lots of bear-related injuries, they are also there to protect the bears. If a bear becomes reliant on human food it will become a nuisance and start raiding campsites etc. This eventually leads to the bear needing to be killed or relocated. So the warnings are good for the bears AND good for the visitors, which means everyone follows them right? No, because people are idiots.

Elk3

Yellowstone also has some other amazing large mammals, notably bison and red deer. The red deer (Cervus elaphus) in the USA are known as elk and they’re bloody huge compared to the red deer we get in Europe (see pictures). Unfortunately the elk have realised that the nicest grass in the park is around Mammoth where the many visitor services (including the park office, staff village, hotel, shops and restaurant) are surrounded by beautifully manicured lawns. This means that one of the most densely populated tourist areas is also covered in female elk grazing while keeping a watchful eye on their offspring asleep in the shade. This presents a real problem to the park rangers who seem to spend most days trying to prevent traffic jams and accidents caused by elk in the road and overexcited tourists. They put up loads of signs warning people to keep their distance from the elk to prevent injury. Of course everyone obeys these warnings right? No, because people are idiots.

Elk4

Finally, there are huge herds of bison roaming Yellowstone. They’re gorgeous and definitely my favourite feature of the park, even if they do have the habit of looking like bears from a distance! They are probably the most problematic animals for the park rangers because they often graze along the sides of the roads. This causes traffic jams when they block the road, but also allows tourists to pull up on the verge and get really close to take pictures. Generally the bison are fairly docile, but during rutting season every year at least a couple of tourists get gored or thrown by male bison. Again the park rangers warn everyone to stay at least 25 feet away from bison at all times. But do people pay attention? No, because people are idiots.

There is always a temptation to blame this on national stereotypes and suggest that people here would never do anything as stupid. Luckily Dusty the dolphin appeared this summer to give us an Irish flavor of idiocy! Dusty is a dolphin that lives in County Clare in a harbour. This summer, because of the unusually nice weather (thanks global warming!), poor Dusty was being harassed by swimmers trying to touch her and ride around on her back like she was Flipper. Of course Dusty is a wild animal so she reacted like a wild animal by attacking a number of people, leaving one woman in hospital with internal injuries. The local authorities repeatedly warned people to stay out of the harbour and to leave Dusty alone, but all summer there were more reports of people getting back into the water with her. Why? Because people are idiots.

But perhaps I’m being a little harsh here? Nothing quite compares to the thrill of spotting your first “something awesome” in the wild, so I can completely understand why people get overexcited (the first time I saw a hummingbird I jumped up and down repeatedly squealing “hummingbird!” which would be fine if I hadn’t also been 27, on my own, and on a guided tour of Alcatraz at the time). However, after that initial rush, the response to a wild animal must be guided by the fact it is wild. Perhaps the problem is that bears, bison, elk and dolphins are charismatic, and we’ve all grown up watching cartoons and documentaries about them so we don’t have a healthy level of fear? Perhaps this is something we need to make clearer in documentaries? In particular I think we need to show how far away the camera is when the beautiful close up shots are taken. Many people visiting national parks are disappointed by seeing an animal at a distance, but this is because we’ve all been conditioned to expect to be as close as David Attenborough appears to be. We also need to be more honest about animal behavior in the wild. Documentaries have a tendency to anthropomorphize animals making them appear unthreatening and cutting out anything too graphic. But in the wild it’s a constant struggle for survival that leaves very little room for altruism. Male lions kill the cubs of other males when they take over a pride; dominant meerkats will viciously attack subdominants that become pregnant, often killing them and their offspring in the process; and chimps will rip the limbs off colobus monkeys (and chimps from nearby groups) and eat them. Nature is “red in tooth and claw” and perhaps we need to make more effort to teach people this before they go to national parks and put themselves, their families and the animals at risk?

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

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Science X-Factor

Im a scientist logo

What is consciousness? Why do we live? Why did the dinosaurs die out? Are tenrecs cannibals? Can we control our dreams? Do you like cake?!

These are just some of the burning questions which I had the pleasure and challenge of trying to answer while taking part in I’m a scientist, get me out of here!  This online competition is science communication and outreach designed for the X-factor generation; school students submitted their science (or otherwise!) –related questions to panels of scientists divided across different zones of research. The students used the resulting answers to cast votes to keep their favourite scientists in the competition. In each round, the person with the fewest votes was eliminated (minus the tense lighting and music which normally accompanies these things) until there was a final winner left standing in each zone of the scientific jungle – and it didn’t even involve eating bugs!

I had some notion of what to expect from following Andrew Jackson’s participation last year but even still nothing prepared me for the all-encompassing addiction I would experience. I thoroughly enjoyed delving into the dusty recesses of my general scientific knowledge, honing my googling skills for some of the tougher questions (thank you Wikipedia!) and, most importantly, developing the fine art of interspersing scientific explanation with liberal sprinklings of smiley faces and emoticons. I was in one of the general science zones (as opposed to the themed space and nanotechnology zones) which left us open to an interesting and challenging array of questions; from what is quantum mechanics (oh how I wish I had more than Junior Cert physics!) to why do we grow more when we sleep ? The scientists taking part were equally diverse in their backgrounds and stages in their research career; my zone included a chemist, mathematician, pharmacologist and neuroscientist so it was very interesting to see how our specialities influenced our answers to some of the more open-ended questions.

One of my favourite parts of the event was taking part in live chats; half-hour sessions with school classes where we were open to anything that the students cared to throw our way. They were great fun and quite intensive; classes of around 30 students all submitting questions at the same time which meant that the chats were a bit like a cross between the ultimate quick-fire quiz round and an exercise in typing speed! I loved the challenge of coming up with on the spot answers to questions ranging from “Are we alone in the universe?” and “How did life begin?” to “What did you like about school?” Varied topics to say the least but my favourite live chat question was definitely “What’s the average trajectory of a swallow” to which I replied “an African swallow or one carrying coconuts?” (You never know when an eclectic knowledge of classic comedy and musicals might come in handy!)

The main aim of the event is to encourage students to take an interest in science, not necessarily with the view towards choosing a science-related career but more to spark their curiosity in the world around them. A big part of this is trying to show scientists as “normal people” – a debatable description at the best of times but hopefully at least it’s a step away from the lab-bound, crazy-haired, mad-scientist stereotype. The dawning realisation that scientists are real people too did produce some funny outcomes – imagine having a sibling who’s older than a scientist!

I hope that the students enjoyed taking part in the event but I know that it was definitely a hugely rewarding experience for me. Aside from writing some articles it was my first foray into the world of science communication and outreach and I’ve definitely been bitten by the bug. There were some really great, difficult questions which were tough but fun to try and answer. I also enjoyed the challenge of losing the jargon while still getting across the important scientific concepts and ideas. I was delighted to win my zone; I hope that my answers had something to do with it although I have a feeling that the combination of an exotic study species, a background in zoology and a cute puppy in my profile picture may have been advantageous in appealing to the teenage demographic…

The competition was a clean sweep for TCD scientists; Shane McGuinness won the Helium Zone, Sinead Cullen came top in the Nanotechnology Zone and Joseph Roche took the prize in the Space Zone.  It’s certainly a good sign for the healthy interest of Trinity staff and students in communicating their research and science in general to a wide audience. This is the second season of the event in Ireland; a spinoff from the highly successful UK event  and the newly added version for engineers. It’s a great event for scientists and students alike and I would highly recommend getting involved. When else do you get the excuse to contemplate anything from cosmic computer programming creators  to some of the really important parts of life?

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

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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

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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

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Join us!

Uncle_Sam_(pointing_finger)It’s that time of year again at EcoEvo@TCD where we start looking for people to apply for Irish Research Council fellowships to come and join us as postdocs or PhD students. These awards are open to anyone, regardless of nationality. Details can be found here(PhD funding) and here (postdoc funding).

But why would you want to join us? I can talk (type?) at length about this but maybe the best people to ask are the students  and postdocs we already have working here. So here are their comments instead!

Thomas Guillerme @TGuillerme

Supervisor: Natalie Cooper (Zoology)

As a French student, starting a PhD in this department was made really easy by the people working here. Not only the academic work and projects are really exciting, but also the social part of the department makes work really easy going and fun.

Deirdre McClean @deirdremclean1

Supervisor: Ian Donohue (Zoology)

I can’t recommend the zoology department enough as a place to do a PhD! This is largely due to the great diversity of projects going on and the close relationships between staff and students. Collaboration is greatly encouraged and there is so much opportunity for this through NERD club, tea breaks and pub trips!  We have a really nice mix of empirical and theoretical projects meaning that we get really different and interesting perspectives on our work, which I think has been great in my development as a scientist.  Being in a small department has a lot of advantages and it means I always find so much support from my supervisor, other PhD students and other staff. Because of the friendly atmosphere and the variety of research groups and backgrounds, lunchtimes, tea breaks and pub visits provide great opportunities for getting input on your work, coming up with new ideas and having debates! There is also a lot of opportunity for teaching, outreach and collaborating with other groups/departments. The campus here is beautiful and right in the centre of town so it’s a really nice place to work and socialize too!

Shane Mc Guinness @S_Mc_G

Supervisor: Anna Davies (Geography)

Without the support, funding and independence provided by IRC funding, my amibitions to study endangered species conservation and human development in Africa would not have been realised. In addition, the increasing integration of the School of Natural Sciences makes this a truly interdisciplinary environment to work in.

Karen Loxton @LoxtonKaren

Supervisor: Celia Holland (Zoology)

From fantastic supervisors to technicians who seem able to solve any problem, the Zoology Dept. has been an amazing place to study for a PhD. Staff are generous with their time and expertise and the seminars and EcoEvo group are a great way to keep up to date with research outside your own. The diversity of projects within the department ensures that pub conversations are always an opportunity to learn something new and interesting.

Kevin Healy @healyke

Supervisor: Andrew Jackson (Zoology)

So far I have really enjoyed doing my PhD in the Zoology department, mostly this is due to the fact that we get the opportunity to work on loads of cool collaboration projects (right now I’m working on a T.rex paper due to a bet in the pub on who could have a dinosaur paper first) but also because there is a very relaxed social vibe to the department as well. I think my development as a scientist over the last two years is also really down to the amount of support from not just my supervisor but all the other members of staff, whether its from our NERD club meetings, going to conferences or just a lively debate at lunch. It also helps that the department is right in the middle of Dublin so there’s plenty of pubs to continue work after 5!

Sive Finlay @SiveFinlay

Supervisor: Natalie Cooper (Zoology)

The Zoology Department is a lovely home for a PhD student. There is a very relaxed, friendly atmosphere with plenty of opportunities to mix with and learn from staff, postdocs and fellow students. We’re a relatively small department but that is definitely to our advantage because you get to know people from diverse research backgrounds and you’re not lost in the anonymity of being yet another student in a large research lab. In the past few years there’s been increased collaboration and integration across the School of Natural Sciences through our NERD club meetings, postdoc talks, weekly seminars from invited speakers and via the EcoEvo blog, all of which are great for getting out of the bubble of being stuck in your own project. There are also plenty of opportunities to get involved in teaching, collaborative projects, fun outreach events and of course a healthy amount of socialising… What’s more, Trinity is a great university with a beautiful campus in the centre of the city – not a bad place to work!

Seán Kelly @seankelly999

Supervisors: Nicola Marples and Dave Kelly (Zoology)

The Zoology Department and the School of Natural Sciences are full of friendly and welcoming students and staff from a great variety of backgrounds. I never fail to find support or advice on my PhD project when it’s needed, whether from my supervisors, other staff or students. The diversity of expertise within the department is a real asset; one that is readily available to you. Integration within and between the various departments is ever increasing and collaboration is greatly encouraged. Lunchtime conversations often turn into lively debates and sometimes lead to new collaborative projects. There’s ample opportunity for teaching experience, group learning and social outreach, as well as socialising, of course.

Sarah Hearne @SarahVHearne

Supervisor: Ian Donohue (Zoology)

I was nervous moving to a new university to study a new field of biology, but I shouldn’t have been. The department is incredibly friendly and welcoming and there is a great spirit of collaboration. This isn’t a place to hide away for three years, it’s a place where discussions are had or ideas spawned over a pint in the pub or during a lunch break. People share their successes and commiserate over failures. Some great science is done as well!

Adam Kane @P1zPalu

Supervisor: Andrew Jackson (Zoology)

The Zoology department has a great group of scientists who are interested in each other’s research which makes for excellent collaborative opportunities. The best advertisement I can give for it is that I don’t dread getting out of bed on a Monday morning.

Katherine Webster

Supervisor: Ian Donohue (Zoology)

Being part of the dynamic and interactive EcoEvo group in the School of Natural Sciences has greatly enhanced my experience at Trinity as a postdoc. From the students to faculty, you gain valuable feedback into your own research while learning about new ideas that expand your own perspectives. Being in Dublin and walking the hallowed grounds of Trinity College certainly adds to the experience!

If you’re interested and have a member of staff with appropriate research interests in mind, please get in touch! Contacts and research profiles of staff can be found here. Note that, unfortunately, the application success rate is fairly low and the applications themselves take a bit of effort to fill in for both the applicant and the academic who supports the application. Because of this we won’t be able to support every person that contacts us. But we promise to be realistic about your chances of getting funding. This is judged on your CV, the project, and the fit of the project to the chosen supervisor. The call opens in November and the deadline is January.

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

Image: Wikimedia commons

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Still Life and Science

Can you draw? Can you draw well? Chances are if you’re a biologist the answer to at least one of these questions is ‘no’. You may have studied art at school, in the same way you took French or Literature, but you figured that as a budding biologist the days of declining verbs, finding meaning in poems or sketching a vase of flowers were far behind you. Then, one day you go to an undergraduate lab session and someone says ‘look at this specimen and draw what you see”.

Draw? But I can’t draw!

I know that this is a common reaction because it was one I had myself as an undergraduate and one I’ve been seeing recently while demonstrating in labs. I found myself trying to explain that you don’t need to be able to draw to do scientific drawing but couldn’t seem to explain satisfactorily what you did need. So I thought I’d take this opportunity to say what I think is important for scientific drawings and then in comments below others more knowledgeable than myself can add their advice.

I guess the first thing to understand is the point of a scientific drawing. Scientific drawings differ from art in that they are not trying to find a ‘soul’ or convey via metaphor some deeper truth. Instead they are trying show accurately and with as much detail as possible what an organism looks like at a given magnification.

In other words, not this:

Fig 1 - Van Gogh sunflowers

but this:

Fig 2 - scientific sunflowers

The reasons for doing this are two-fold. One is for your own benefit. You may find yourself studying a multitude of specimens in detail for a period of time but if you have to stop the work for some reason then without accurate notes you will have no idea what you’ve been doing (this goes for lab notes in general, not just drawings). The other reason is to show other researchers what you are describing in text. A picture is worth a thousand words, so the saying goes, and given the technicality of the language of many fields of science, it also makes understanding easier. You may think that photography has superseded the need for line drawings but surprisingly not. Photos that capture all the details required can often be extremely hard to take: getting the exposure, angle and perspective correct can be very difficult, especially for small or otherwise fiddly objects.

I realise that the scientific drawing above is beyond the skills of most of us, but there are ways to achieve a certain level of technical ability without possessing any artistic merit. If I may indulge in a personal anecdote, I cannot draw. I gave up art at school as soon as I was allowed and in that time I never progressed beyond drawing three-dimensional boxes (though I was really good at them!). Yet I have done a scientific drawing that was suitable for publication1:

Fig 3 - anglerfish

The point is not to gloat (honestly, who would gloat over that!) but to say that if I can do it, anyone can!

So, how do you do it? There are a few pieces of equipment that are essential in my view. These are:

  • Sharp pencil (a ‘clicky’ pencil with a hard (HB) lead is ideal)
  • Plain paper
  • Ruler
  • Eraser

The ruler may seem strange at first but if you are making any attempt at accuracy proportions are key. I’d even go so far as to say if you have one to hand, use a protractor to help with angles as well.  The main problem I’ve seen is students getting the proportions wrong because they are drawing solely by eye. Measure the size of parts and translate that to the page. If you can do a one-to-one scale then great but if that’s not possible then factor up or down as necessary. Make notes if you have to. To draw the illustration above I had a page covered in all the various measurements, from the length of the appendages (it’s the lure of an anglerfish, if you’re wondering) right down to the size of the larger spots. The purpose wasn’t to make a beautiful illustration (which is good as it isn’t) but to show other researchers as clearly as possible the key feature used in identifying the fish.

It’s really helpful if you can poke around the specimen you are trying to draw, if possible. Something may look completely incomprehensible but if you lift it or tilt it, it can often suddenly make sense. It’s really hard to draw what you don’t understand. Label parts if you can, especially if you’re making a first draft. The more information the better. You never know what detail may become important and if you haven’t noted it then you may regret it (I had to go half-way round the world to re-examine that fish because I didn’t make good enough notes and drawings the first time).

It will take several attempts to do a really good illustration and obviously in labs you don’t have that sort of time but you can still use them to start developing your skills. You can also practice. It’s really easy: just find a biological object (shells are really good) and try and draw it as accurately as possible. You will get through lots of paper, rub out lots of lines and probably swear and get frustrated, but you can draw scientifically. And, which is ultimately the real reason for doing scientific drawings, the close study required to achieve this will help you understand the specimen in deeper and more complete way.

Good luck and enjoy!

1. Hearne S. (2009) First record of the anglerfish, Himantolophus appelii, from the Falkland region. JMBA2 – Biodiversity Records. 2: e152

Author:

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

Image Sources: Wikicommons and Sarah Hearne

 

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Blog-tastic!

Seminar

Andrew Jackson and I started a new module this year called “Research Comprehension”. The aim of the module is simple: to help students to develop the ability to understand and interpret research from a broad range of scientific areas, and then to develop opinions about this research and how it fits into the “big picture”. In our opinion, this is perhaps the most important thing an undergraduate can get out of their degree, because no matter what you do when you graduate, in most jobs you will be expected to read, understand and interpret data. Often this will be in a subject you are unfamiliar with, or use unfamiliar methods or study organisms. So being able to understand this information is key!

The module revolves around the Evolutionary Biology and Ecology seminar series in the School of Natural Sciences, so the topics are broad and cover whole organism biology, molecular biology, genetics, plants, and animals etc. Students attend the seminar on a Friday and read some papers sent on by the speaker. There is then a tutorial on a Monday with a member of staff who has interests in the area of the seminar. This gives everyone a chance to clear up any confusion and to discuss what they liked (and disliked) about the seminar. The continuous assessment for the module is in the form of the blog posts we will post here. Thus the module also aims to improve the students’ abilities to communicate all kinds of scientific research to a general audience, a skill that is currently in great demand.

From next Wednesday onwards we will select a few blog posts to put onto EcoEvo@TCD. These may not necessarily be the posts that get the best grades, but they’ve been chosen to reflect the diversity of angles the students have taken to communicate the parts of the seminar they found most interested. Overall we’ve been extremely impressed with the quality of their blog posts, so we hope you enjoy reading them!

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

Image Source: Jorge Cham, www.phdcomics.com

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Kenya- A Summary through the vegetation

Campsite at Ol Pejeta, with Acacia xanthophloea in the background.
Campsite at Ol Pejeta, with Acacia xanthophloea in the background.

During the first week of November I travelled to Kenya to help out on the Tropical Field Ecology course, run by Ian Donahue in the Zoology Department.  Final year students from Zoology, Environmental Sciences, and Plant Sciences attended, and I was the postgraduate representative from the Botany Department.  While I should under no circumstances be considered a true Botanist-I study plant-animal interactions, and my botanical skills are mediocre at best- I did my best to learn about the amazing tropical flora of this region.  I’m sure others will write about the trip in detail, but I thought I would summarize our experience using the dominant or interesting plants we saw in each place we travelled.

Day 1&2- Arrive in Nairobi: After spending the night in the United Kenya Club, we awoke to a 5 hour drive north to Laikipia County.  Along the way the most striking plants were ornamental and known to a number of the students already- for example, colourful Bougainvillea was visible from quite a distance, as were the beautiful flowering Jacaranda trees- neither of course are native to the region.

Day 3-Ol Pejeta Conservancy, Laikipia County: We camped for the next two days in Ol Pejeta, and although we experienced quite a bit of rain, it was one of the most beautiful places I’ve ever seen.  The campsite was on the river and surrounded by Acacia xanthophloea, known to the locals as “Yellow fever acacia” for its medicinal properties.  It has a yellow-green bark which makes it quite distinctive.  On game drives we saw a lot of scrubby shrub species, none in flower.  It was difficult to identify many of the species in the conservancy but we were told many of them belong to the genus Euclea.  We also got our first glimpse of Solanum incanum but more on that later.

Solanum incanum at the Chimpanzee sanctuary in Ol Pejeta
Solanum incanum at the Chimpanzee sanctuary in Ol Pejeta

Day 4- Nakuru: Compared to Ol Pejeta the flowering flora here was a breeze to identify! Although a lot of it comprised invasive species, such as Lantana and Datura species, and of course the conspicuous Solanum incanum (also known as Sodom’s Apple).  S. incanum gives the management at Nakuru serious trouble, growing uncontrolled in areas that are over grazed or disturbed by humans.  In addition to the invasives we saw a lot of Leonotis mollissima and identified a lovely shrub called Tarchonanthus camphorates from its camphor scented leaves.

Day 5-11-Baringo County: And finally, after quite a lot of driving (during which we saw some impressive Euphorbia candelabra specimen), we arrived in Baringo County.  Our first day here we went for a hike at Lake Bogoria, and spotted two species of interest.  First, the indigenous Adenium obesum, or Desert Rose.  Some of the students carried out their mini-project on the nectar secretion and flower visitation of this species, and found nectar volume varies with time of day.  Second, we saw Salvadora persica, known as the “toothbrush tree.”  Our local guide told us people chew the twigs to promote dental hygiene.  Throughout the county, two new species of Acacia were also evident- Acacia tortilis (The Umbrella Thorn, accurately named after its shape) and Acacia mellifera.  Women in the area highly value A. mellifera because the honeybees they keep apparently favour it for making particularly sweet honey.  And finally, one cannot forget to mention the damaging invasive Prosopis juliflora.  Native to Mexico and Central America, it was introduced to try and control soil erosion and now has spread throughout the county.  It is difficult to remove as it can regenerate from the roots, and is not particularly useful as fuel, food for livestock or fencing.

Adenium obesum, Desert Rose at our campsite in Baringo, Robert’s Camp
Adenium obesum, Desert Rose at our campsite in Baringo, Robert’s Camp

This description is simply the most obvious vegetation we saw on the field course.  The diversity of flora and fauna was overwhelming and I think the students, demonstrators, and staff alike were impressed and awed by the environments we were fortunate enough to experience.  Kenya is truly an amazing place!

Author and Picture Credits;

Erin Jo Tiedeken, tiedekee[at]tcd.ie, @EJTiedeken

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SQUIRREL PLAGUE! Or “Don’t hug a dead squirrel”

Squirrel

During my PhD I worked on the morphological evolution of New World monkeys, phyllostomid bats, Australasian possums, and ground squirrels. For some reason the only part anyone outside academia (and some people in academia) remembers is that I like squirrels. This means that whenever there is a squirrel-related news story, around half a dozen people send me a link and/or want my opinion.

So this July I got sent a lot of copies of this story: “Squirrel infected with the BUBONIC PLAGUE closes major US campgrounds” (the Daily Mail clearly decided the words bubonic plague weren’t shocking enough so they put it in capital letters; sophisticated journalism at its best).  This was less shocking to me than most people expected, because I have an interest in zoonotic diseases (diseases transmitted from animals to humans) and was already aware of the continued existence of plague. However, in light of the over excitement in the media, I thought I’d write a quick blog post about plague and try to clear up some of the confusion.

When most people think of bubonic plague they think of the Black Death in the 14th Century. This is definitely the most famous and most devastating outbreak of plague – it wiped out 30% of the population of Europe and contributed to major changes in society and agricultural practices across the continent. Other famous outbreaks include the Great Plague of London in the mid 1600s which only ended after the Great Fire of London in 1666. Improvements in sanitation have all but eliminated dramatic outbreaks of plague in the developed world, but it is still is a significant problem in Africa (particularly in Madagascar and the Democratic Republic of Congo), Asia and South America, which report around 2000 cases every year with a global fatality rate of 5% to 15%.

There are three major forms of plague: bubonic, septicaemic, and pneumonic. They are all caused by the bacterium Yersinia pestis but have different symptoms, fatality rates and transmission modes. Bubonic plague is the “traditional” Black Death version of the plague with the black necrotic swellings which lead to blood infections, bleeding, shock, organ failure and eventually death. Septicaemic plague has all the same symptoms but without the initial swellings. In both bubonic and septicaemic plague the bacteria are passed from host to host via flea bites, and both are fatal around 50% of the time if no antibiotic treatment is given. Pneumonic plague on the other hand, has an almost 100% fatality rate if untreated, is transmitted by inhalation of airborne droplets, and mainly affects the respiratory system. So really nasty stuff! Luckily most strains of Yersinia pestis respond well to antibiotics.

Although it’s not a major problem because outbreaks are rare and plague can be treated with antibiotics, the disease is still endemic to the southwestern states of the USA. This means the disease is naturally found there. The natural reservoir population for the disease consists of ground squirrels and other small rodents. Often outbreaks occur in humans after a major outbreak in the squirrels results in humans handling dead or dying squirrels. A few years ago a case in a little girl in the USA was due to her finding a dead squirrel and giving it a decent funeral! So unless you go around playing with dead squirrels, there is very little chance of you catching the plague. Before you panic about that dead squirrel you picked up last week, note that when I say “squirrel” I’m referring to a group of rodents (technically called the Sciuridae) that contains just under 300 species (depending on how you count them!), two of which are the red (Sciurus vulgaris) and grey (Sciurus carolinensis) squirrels we have here in Ireland. Mostly the squirrels infected by plague are ground squirrels, not the tree squirrels we’re all most familiar with. Ground squirrels, unsurprisingly, live on the ground and in burrow systems and include things like marmots, prairie dogs and chipmunks. This means that unless you’re handling some dead exotic migrant squirrel, in Europe at least, you’re probably fine! In summary, all fine, totally natural, totally treatable by antibiotics, nothing to see here, DON’T PANIC!

This post was meant to be all about making everyone feel better but then I ended up reading the World Health Organisation (WHO) website. After all this positivity, here’s the scary bit! Naturally multiple-drug-resistant strains of the bacteria have been identified in Madagascar, and antibiotic resistance appears to be easily transferred between bacteria via plasmids in the flea mid-gut. So unfortunately the age of easily treating plague with antibiotics may soon be over. I was also a bit puzzled by the WHO website because although there are quite a lot of diseases out there, WHO has vaccine development programmes for only a few. One of these diseases is the plague. It turns out that bubonic plague is a big worry because it could be used as an agent of biological warfare. In fact, historians suggest that plague was one of the first biological weapons; soldiers would throw plague-infected corpses over castle walls during sieges in the 14th century.  More recently, the Japanese forces near the end of World War II had devised “Operation Cherry Blossoms at Night” to send kamikaze bombers with the plague to infect San Diego, but were stopped by the atomic bomb being dropped on Hiroshima just a month before the planned attacks. The USA and USSR also experimented with aerosolized plague in the 1950s and 1960s, before the Biological Weapons Convention (BWC) was passed in 1972 forbidding offensive research into biological weapons. However, not all countries or organisations believe in the goals of the BWC or the Geneva Convention, and aerosolized, antibiotic resistant, pneumonic plague, which as I mentioned above is almost 100% fatal if untreated, remains one of the most frightening and deadly, potential biological weapons around, particularly given the high mortality rate and ease of rapid person-to-person transmission. Something to think about next time you try and hug a dead squirrel…

Author:

Natalie Cooper: ncooper[at]tcd.ie

@nhcooper123

Photo source:

Wikicommons