Category: Perspectives

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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

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Christmas Animals

ChristmasAnimal

Would there be a Christmas without animals? It seems like a silly question but think about it; so many of our holiday traditions involve animals in some way. There are the obvious participants; the poultry, pigs, lambs and, in some countries, fish which will be the highlights of millions of Christmas dinners. Indeed, the Christmas story as we know it could not have happened without animals; Mary and Joseph were unlikely to have reached Bethlehem in time without the aid of their “little donkey on the dusty road”. Tucked away in their manger, it would have been vacant and lonely without the “cattle lowing” (although Pope Benedict’s suggestion from last year created some doubt around the traditional cast of manger characters). Without animals, the shepherds would have missed their angelic visitor and we would have to change their song too (although fortunately “watched their flocks” can be easily tweaked to “washed their socks”…). Finally, without their camels the three wise men would have been highly unlikely to reach Bethlehem by the 6th of January. They would have either been significantly delayed, in which case sad Christmas trees long past their glory days would now droop in houses around the world until the spring, or they may not have completed their journey at all and we would lose the annual joy of generations of school children attempting to pronounce the words frankincense and myrrh with gusto.

Difficult as it may be, it is still theoretically possible to imagine a vegetarian Christmas or an animal-free version of the nativity. However, there is one integral part of Christmas which could absolutely not happen in any possible way without the participation of the most important holiday animals of all; reindeer.

Santa didn’t always travel by reindeer. St. Nicholas, the 3rd century Turkish bishop who (along with some help from Coca Cola) is the foundation of our modern views of Santa Claus, certainly didn’t have any reindeer. In Holland, St. Nicholas still brings presents on the 5th of December and, instead of reindeer, prefers to travel by means of a white horse with the help of “six to eight black men”.

Reindeer first came on the scene in two children’s books from the early 19th century, the most famous of which was Clement C. Moore’s The Night Before Christmas. Published in 1823, Moore was the first person to reveal the reindeers’ names; a very important service; imagine the embarrassment if we had to address our reindeer food presents to “whom it may concern” instead of to Dasher, Dancer, Prancer, Vixen, Comet, Cupid, Donner or Blixen directly.

Rudolph first joined the group in 1939. In the increasingly urbanised and atmospherically polluted 20th century, Rudolph’s luminous nose was definitely an asset for Santa’s night time navigation (and of course the constant red light helped him to comply with new low-flying aircraft identification regulations). Rudolph’s importance was exemplified by his own theme song written in 1949. Rudolph’s red nose is often assumed to be a natural bioluminescence, making him unique among terrestrial vertebrates and justifying the provision of carotene-rich carrots as an important dietary supplement to the normal reindeer diet. However, new thermographic images from Lund University have revealed that Rudolph’s glowing nose seems to be a by-product of the constant blood supply which is necessary to prevent the exposed, sensitive skin from freezing.

Similarly, recent research has also confirmed that reindeer’s eyes are seasonally adapted to low light levels so they are certainly well-suited to their night time global navigation duties. Santa clearly picked the right animals for the job.

Incidentally, it’s not clear whether we should be referring to Rudolph or Rudolpha. Santa has a well-deserved reputation as one of the first equal opportunities employer and the fact that he hasn’t felt the need to clarify the reindeers’ genders (or to preferentially hire naturally winged steeds for the task at hand) just confirms his exemplary egalitarian approach to employment practice.

So whether you’re feigning gratitude for some welcome gift, enjoying the sanctimonious pleasure of an extended family gathering or just settling down to watch the Strictly Come Dancing Christmas special (I’m sure it’s not just me…) spare a thought this Christmas for the animals past and present, edible and domesticable, mythical and magical which make our holidays so special.

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

Image source: Wikicommons

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Good, Better, Best

discipline2

Many aspects of human nature seem to frustrate our ideal of a modern society. This is especially true of our morality. We seem to have evolved a brain with two systems relevant to moral behaviour. The first, more ancient component is automatic, judging things as disgusting or inherently wrong very quickly; the second is our slower acting higher-level thinking which has a controlled reasoned process. However the two are not independent, with our more modern system taking its cues from the more primitive part. An evolved morality does suggest that there is no absolute right or wrong, rather it promoted behaviours conducive to fitness.

World peace is unlikely when our moral intuition works on the acts/omission doctrine. This is the doctrine that differentiates between circumstances when we actively perform an action and when we neglect to do it. A person is deemed a murderer if they push a person off a bridge but isn’t if they, by omission, fail to prevent the death. The parallels to people outside of our moral circle, in the developing world, for example, are obvious.

Another serious moral shortcoming is our failure to cooperate, which is most frequently explained through the tragedy of the commons i.e. our inability to invest in the long term interest of the group owing to our rational self-interest. Global warming is one notable problem that is proving difficult to combat because of this inherent tendency.

The free-rider problem is also ubiquitous, whether it is a rich tax dodger or illegal welfare claimant. The majority of us pay a cost for some benefit while a minority piggybacks on the benefits without having to pay a thing. Hardly fair. We have evolved mechanisms to deal with such cheats, for example through indirect reciprocity, but it would be far better if there was no need.

All of this is a précis to the main topic of this post. As we gain more insights into the neurology and psychology of our morality we’ll be able to manipulate it for our own (hopefully) positive ends. This is quite clearly a controversial idea but we already treat people to make them more moral albeit in a crude way, notably chemical castration of sex offenders. Is it really wrong to stop our parochial and short sighted biases?

Julian Savulescu is one proponent of human moral bioenhancement. He argues that humanity’s future is not safe in our own hands because of our inherent moral failings. His suggestions are novel to say the least. We could look to enhance our sense of altruism and trust by manipulating oxytocin levels which would make our prospects rosier. It could also be the case that those in power create a population of exceedingly trusting sheep over which they could rule. His moral philosophy is from the utilitarian school of thought – the greater good. And this school seems most in line with an evolved morality where there are no absolutes but that’s not to say there aren’t enormous problems with it. How do we convince people to take a supplement that will change their very nature when they are opposed to it?

In Brave New World, it is the people who eschew the psychological benefits of the drug soma who are made out to lead a more authentic existence. But can we afford to live the life of savages when it could lead to our annihilation?

Author: Adam Kane, kanead[at]tcd.ie, @P1zPalu

Photo credit: artofmanliness.com

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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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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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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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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

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How Good is the Fossil Record?

crinoid

One of the projects I’ve been working on recently has concerned diversity in the fossil record. In broad terms I’m looking at how diversity has changed over the last 540 million years, a period known as the Phanerozoic which starts at the Cambrian explosion and continues to this day. I want to try and understand what causes the periodic increases and decreases in diversity.

I’m not a palaeontologist, so this work has involved a massive learning curve in order to understand how we know what we know about the fossil record. What I’ve learned has led me to have an enormous respect for palaeontologists, but to also wonder whether some of the claims made on the basis of evidence from the fossil record may not be slightly overstated.

If we compared the fossil record to a court trial, I’d argue that the public perception is that the fossil record is rather like the court transcript: a full and complete record of the history of life on earth. Scientists outside the field of palaeontology probably understand that this is not true, and may liken it to more of a newspaper report on the trial: summarising, missing some details but the key facts are in place. The more I look into the fossil record, the more I think it seems like the hear-say testimony of an unreliable witness: heavily biased, missing important facts and giving probably erroneous information.

Before I get angry palaeontologists shouting at me I want to emphasise that that for short timescales or small areas I think the fossil record is brilliant and we can learn a lot about species turnover and ecosystem development. My concern comes from combining these short timescales and small areas and then using them to produce long timescale, global patterns of diversity. While it may seem like this is a sensible way to produce this data – who could possibly sample the entire earth for the entirety of the fossil record by themselves? – there are a number of so-called sampling biases that I feel make this approach potentially troubling. And while I have seen a great deal written about these biases and the efforts to reduce their effects, I have also seen research that makes me think these biases are impacting the data in ways we cannot predict.

So, after all that build-up, what are these biases? You’ll forgive me if I don’t discuss them all here, there are so many. Instead I’m going to split them into two groups and discuss these groups in very broad terms, focusing on the ones I think have the potentially biggest impacts on the patterns of diversity at the global scale. Proper palaeontologists have used a variety of different groupings, but I’ve grouped them into taphonomic biases and taxonomic biases. Taphonomy is the process of fossilisation but in this discussion it will also involve the process of the discovery of fossils. Taxonomy is the naming of species and there are a surprising number of biases that result from this seemingly simple process.

The most obvious taphonomic bias is that of the potential for fossilisation. It has been estimated that less than 10% of living species would end up in the fossil record and it would be heavily biased towards those organisms with bones or shells [1],. Many of the fossil diversity analyses are performed on molluscs as they have a good fossil record, so you might think that this would remove this problem. But the type of fossilisation affects how well an organism is preserved, if at all, and this affects molluscs just as much as other animals [2]. Plus, using molluscs assumes that they are a good model and representative of all organisms over all time which seems to be asserted without much evidence.

Another taphonomic bias is that of true sampling. At one end, not all environments are fossilised and at the other, not all fossil beds are studied by palaeontologists. In between, some fossil beds may be eroded over time and others may never reach the surface to be exposed for study. This leads to an effect called the ‘Pull of the Recent’ [3] whereby diversity increases towards the present day simply because there are more rocks available to study; the oldest ones have eroded, and the ones left are fewer in number the further from the present you go.

This sampling is not only biased in time, it is biased in space. There is a global trend in biodiversity, with highest levels at the equator and lowest at the poles, called the Latitudinal Diversity Gradient (LDG) [4]. This trend occurred throughout much, if not all, of the Phanerozoic and means comparisons of fossils between time periods must be from similar latitudes otherwise changes will say nothing about global diversity. While we may talk in terms of ‘global diversity’ it is often based on limited samples that may be predominantly from the tropics in one time period and temperate latitudes in another, yet this is rarely considered as a compounding factor when diversity is discussed.

Taxonomic biases are no less concerning. Naming fossils is more complex than naming living organisms, as the names must be based purely on the (potentially incomplete) skeleton. It is increasingly common to find living organisms that look identical but are genetically distinct species, and conversely organisms that look very different but are simply displaying phenotypic plasticity [5] yet fossils are named on the basis of their (potentially misleading) morphology which can significantly affect diversity estimates. Then there are problems of widespread fossils being given different names in different countries, or long-lived fossils being given different names in different geologic periods. Finally, there is the fundamental problem that the fossil record shows species evolving, and someone has to decide if and when a new species has formed and a new name applied. This will present itself in the data as an extinction and origination event, even when the population may not have changed in size or location.

These are just the very tip of an iceberg of biases. It may well be that palaeontologists have answers to all these biases and I have just failed to find the relevant literature. So far all I have found seems to be the claim (hope?) that all the biases will cancel each other out, leaving the true biological signal visible. I can’t be so certain. Indeed, my greatest fear is that the patterns of diversity are nothing more than the product of these biases and have little relation to the actual changes of diversity over the history of life on Earth. Reassurances to the contrary would be most welcome!

1. Nicol, D. (1977) The number of living animal species likely to be fossilised. Florida Scientist. 40, 135–139

2. Martill, D. M. (1998) Resolution of the fossil record: The fidelity of preservation. In The Adequacy of the Fossil Record (Donovan, S. K. and Paul, C. R. C., eds), pp. 55–74, John Wiley & Sons

3. Raup, D. M. (1972) Taxonomic diversity during the Phanerozoic. Science. 177, 1065–1071

4. Hillebrand, H. (2004) On the generality of the latitudinal diversity gradient. The American Naturalist. 163, 192–211

5. Bennett, K. D. (2013) Is the number of species on earth increasing or decreasing? Time, chaos and the origin of species. Palaeontology. in press,

Author and Picture Credit:

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