May 2013 - EcoEvo@TCD

31/05/2013

Who’s afraid of the big bad wolf?

In popular culture, especially literary references, wolves are usually sly, cunning and vicious. Think of the fairy tale wolf villain who used his drag queen and voice modulation skills to fool Little Red Riding Hood into thinking that he was her aged grandmother. Some literary wolves are more than a little bit gullible; thwarted in his attempts to demolish a house of brick, the Big Bad Wolf resorted to a chimney entrance route to reach his porcine prey. Not the wisest option; he should have known that the Three Little Pigs had plenty of straw and sticks to kindle a substantial fire.

Captive wolves can be just as cunning as their fairy tale counterparts. RTE’s series on Dublin Zoo featured amazing footage of an extensive tunnel system the wolves had excavated below their exhibit. They were slowly making headway towards the boundary fence and would have eventually escaped into the Phoenix Park had their attempts not been thwarted by vigilant keepers. Surely these wolves’ valiant efforts deserves a theme tune…

Anthropomorphic representations of wolves are undoubtedly influenced by their status as carnivores. It’s easy to project evil characteristics or motivations onto animals that hunt and kill cute and placid grass-munchers. In contrast, can you think of any stories about evil or menacing herbivores? (What exactly is an evil giraffe?)

Interestingly, though, our literary biases against carnivores only extend to some species. Think of all the children’s books about cute and cuddly polar bears; somehow they manage to gloss over the blood and gore at the end of this incredible video.

Cultural biases and anthropomorphic labelling of wolves as “evil” or “cruel” may even contribute to some of the staunch opposition to wolf reintroduction and management programs. Wolves are sometimes perceived as vicious killers with no role in or value to an ecosystem. This is in contrast to other sympatric predators, such as cougars, which can be equal if not greater threats to both humans and livestock but don’t elicit the same controversies or opposition to their management or conservation. The difference in our perceptions of these predators seems to be historical. It’s much easier for ranchers to accept and cope with the threats from cougars than to contemplate or deal with the problems associated with reintroducing wolves back into areas which formed part of their historical range.

I’m not attempting to dismiss or belittle the very legitimate concerns and problems associated with managing and protecting wolves. But perhaps if we change how we perceive and depict wolves in our stories and culture it would help to rejuvenate their image and re-cast them as no more evil or menacing than other predators with which we have learned to cope.

I think we need to boost wolves’ PR. The Twilight series is certainly playing its role in this mission; wolves have never been so popular among teenage girls. Despite these efforts, we need more positive cultural and literary links to wolves. Perhaps a new series of children’s books about “Winston the wistful wolf” or an uplifting Disney wolf cub coming-of-age story would do the trick? These majestic creatures should not suffer the fate of perpetual villain type-casting .

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credit

Wikimedia commons

29/05/201318/02/2019

Do badgers play Friesian tag?

While there is irrefutable evidence for the transfer of bovine TB between badgers and cattle, the mechanisms of transfer are not clearly documented. In order to reduce such transfer, it is obviously important to understand how infection takes place.

With such questions in mind, data from a study of free-ranging badgers was combined with detailed records of paddock use by cattle. Each study badger was carrying a personal GPS unit on a tailored collar, so their movements could be monitored to within a few meters. The paddock use of the cattle was recorded on a daily basis. The data were combined, using mapping software, such that a daily log could be constructed for badger and cattle activity. Continue reading “Do badgers play Friesian tag?”

27/05/201327/05/2013

IUCN Red Listing Ecosystems Workshop

Many of us attended a fantastic seminar on Friday the 17^th of May, given by Dr Ed Barrrows – IUCN Red List of Ecosystems: An evolving tool for risk assessment, priority setting and landscape action. Dr Ed Barrows is a former graduate of Trinity’s Zoology Department and is currently the Head of Ecosystems at the IUCN. The focus of his talk was to introduce us to the new risk assessment criteria developed by the IUCN to assess ecosystems. This will ultimately provide the world with a Red List for Ecosystems. We were all familiar with the concept of a Red List for Species but this was the first time we had been introduced to concept of a standard global assessment of risks for entire ecosystems or “higher levels of biodiversity”. First we had a great introduction into the new ecosystem assessment tool developed by the IUCN. Ed brought us through the process behind the model and the need for such a tool. Incorporated in the model was the interesting concept that of ecosystem collapse. When does an ecosystem go beyond recovery and change into something else.

A well deserved cup of coffee and great pastries helped us to digest and process this information.

Following this, a number of the lucky ones who had signed up for the workshop traipsed over to the SNIAM building where we were in for a treat. Ed was hosting a two hour workshop to give us all some practical experience of applying the model and carrying out a risk assessment on an Irish ecosystem. There really was a great mix of people attending from permanent Trinity staff, post docs, master’s students, undergraduates and members of various NGO’s.

We were divided in to four groups. The model uses four distributional and functional symptoms to assess ecosystem risk. Two of the groups were to look at the criteria A & B (distributional) and the other two C & D (functional). Ed explained to us that the process of evaluating a habitat would normally take over four months and extensive amount of backing data. He then proceeded to tell us that we had two hours and two scientific papers with which to assess maybe one of the most politically sensitive habitats in Ireland “Peat lands”! A lively debate ensued as the two groups from each section gave their results and the reasons as to why they come to those conclusions. The final discussion looked at the fifth criterion which estimates the risk of ecosystem collapse and assigns it to critical, endangered or vulnerable – I think there are still people arguing over it…

Author

Caoimhe Muldoon: muldoocs@tcd.ie

Photo credit

Wikimedia commons

24/05/2013

May I take your order?

My PhD involves studying the foraging behaviour of vultures. So far I’ve done theoretical work and also had the luck to get some second hand empirical data. But I’d like to be able to get some field data first hand. To that end I’m setting off to Swaziland on Saturday with the intention of building a vulture restaurant and a walk-in trap. The first item takes a little explaining. Vultures are carrion feeders, which means their food source is unpredictable, the bird never knows when the next wildebeest is going to drop dead. So they’re quite sensitive to declines in food availability. But a vulture restaurant is a conservation tool that acts as a supplementary feeding station for the birds. The people organizing the restaurant can deposit carrion at the site thereby providing an extra food supply for the vultures. This is done to keep the birds within an area, to feed them during times of food scarcity or in my case to aid in their capture.

Alongside the restaurant we’re going to build a walk-in trap, a simple structure that the birds walk into before we close the door behind them and have a PhD’s worth of data points. Well, it’s not quite that easy. I want to be able to find out to where these birds are foraging at a high temporal resolution so we will be putting GPS tags on the vultures once we capture them. This means some poor soul will be entering the trap and extracting the birds one by one, each animal getting tagged before being released back into the wild. I should stress this has been done before on many occasions and the birds are all freed within minutes without any ill effects.

So far a lot of research done in this area provides us with broad-scale movement patterns. With my finer scale data I’ll hopefully be able to pick out some quite specific aspects of vulture foraging behaviour. Wish me luck!

Author

Adam Kane: kanead@tcd.ie

Photo credit

Wikimedia commons

22/05/2013

Science be praised, please cure me of my Yoda Complex

My former PhD student, Luke McNally and I authored a paper published recently showing how “Cooperation creates selection for tactical deception”. Using a combination of mathematical models and analysis of empirical data from 24 primate species, we show that acts of deception are more likely to occur when the individuals in the group show greater cooperation. In other words, deception and cooperation go hand-in-hand. Perhaps not a surprising result, as Rob Brooks recently pointed out in a very accurate and nice blog post on our paper, but the evolutionary forces that might maintain deception in society have not been previously described.

We have enjoyed some media coverage with this paper, including some international science slots, a bit of national radio and Rob’s blog post. I take some mixed pleasure in the fact that a creationist website picked up on both our paper and Rob’s post. Its something of a tongue-in-cheek achievement to have caught their eye given my total opposition to creationism in all its forms. I’m also quite proud to have earned a “Darwin baloney” award (which I might add to my website as a badge of honour assuming I’m not infringing copyright). Im also intrigued to have the mental disorder “Yoda Complex” bestowed upon me by this group, even if it is not the Urban Dictionary definition but rather their own invention because “because we thought of it independently” (Editor’s comment in http://crev.info/2013/05/evolutionists-confess-to-lying/). So happy with this flattery than I now tweet under @yodacomplex.

Ordinarily I would steer clear of getting sucked into arguing with such groups, but their article just annoys me. I’m even more annoyed that I can’t reply to their post on their site without signing into their site, and registering with them is a bridge too far. Equally frustrating is their anonymity which makes directing my counter-arguments somewhat indirect.

The consequence of their argument is that “if lying evolved… how are readers to know who is telling the truth?” which leads them to the title “evolutionists confess to lying” (http://crev.info/2013/05/evolutionists-confess-to-lying/).

The basis of their argument goes:

“Imagine a liar so skilled, he convinces his listeners that he is 100% against the worst dishonesties in politics, public relations and propaganda. He tells you he wants to achieve enormous social good to provide a better understanding of how lying evolves. Now, add to it that he is self-deceived. Doesn’t his credibility implode? How could one possibly believe a word he says?”

How can one believe what a person says? This is exactly why we have science. Our results are open for all to examine and check. The results might be incorrect (but we are confident in our analyses), but until someone shows us exactly where we have gone wrong, then we can take them as being a true and fair reflection of our study system. Our mathematical model shows under what circumstances deception (lying) can be sustained in an evolutionary sense in any society subject to a cooperative based reward system (in this case a system governed by the Iterated Prisoner’s Dilemma). The prediction from the model is that mechanisms that might enforce cooperation (such as only cooperating with other co-operators and spurning those who cheat) create a niche where lying can profit and proliferate. Our analysis of data from 24 primate species backs up our theoretical model, showing that the more likely a species is to engage in cooperative acts, the more likely deception is to occur in their society.

The creationist author goes on to make a major error in interpreting the whole basis of the study of the evolution of social behaviour.

“In the evolutionary world, there is no essential difference between cooperation and deception. It’s only a matter of which side is in the majority at the moment.”

This is just plain incorrect, and is the entire basis for their spurious argument. In the study of social behaviour (irrespective of evolution) there is indeed a fundamental difference between cooperation and deception (although I think they really mean defection here, with deception being a means to hide ones defection in the wording of the Iterated Prisoner’s Dilemma). In the Iterated Prisoner’s Dilemma, and related games like the Snowdrift Game, cooperation is the act of assisting another individual so as to share a reward. Defection on the other hand is the act of cheating on the other person in the game so as to walk away with the entire reward for themselves. It is absolutely not a “majority” based definition. Deceivers in our model try to trick co-operators so as to walk away with their share too by convincing them that they intend to cooperate. The kool-aid scenario that follows in that blog post is just not relevant since it invokes a semantic argument about how the players choose to define cooperation and defection that is simply not present in these evolutionary models of social behaviour. All the author has done is to flip the labels of co-operators and defectors. The outcome of their scenario would be that the poisoners (who are actually the defectors as per any sensible definition of their behaviour in cooperative game) would kill all the co-operators leaving only themselves. Indeed, this matches the fundamental prediction of the evolutionary models which offer “defect all the time” as a consistent stable end-game scenario. It is the goal of most evolutionary studies of social behaviour to learn what mechanisms exist in societies that mean we don’t get stuck here, since it is clear that many primates, including humans, have a much more cooperative society than that depressing outlook.

“Since all these evolutionists believe that lying evolved as a fitness strategy, and since they are unable to distinguish between truth and lies, they essentially confess to lying themselves. Their readers are therefore justified in considering them deceivers, and dismissing everything they say, including the notion that lying evolved.”

This is the rather annoying consequence of their incorrect logical arguments. We can and do distinguish very clearly in our models and reasoning between truth and lies – at least in these models we do. Also, just because we point out that lying can have an evolutionary selective advantage (which is hardly surprising), surely doesn’t make us liars? I can’t see what the mechanism there could possibly be.

Just to end, I have to say that it is really difficult not to ridicule this type of article. The reasoning is just so off-the-wall, based on a manipulation of what science is all about, and with a really nefarious motivation running through it of debunking science for the true believers. I did laugh, I did sneer, (and I did take @yodacomplex as a twitter account, and I love it); but, I have tried here to avoid sneering since they use that against us (see the comments under their article). In fairness though, giving us a “Darwin Baloney” logo, and administering a mental health disorder on us (even if they made it up themselves) is pretty much name calling and sneering in my book – even if I am rather flattered to have acquired their attention.

Author

Andrew Jackson @yodacomplex

Photo credit

wikimedia commons

20/05/201320/05/2013

The VIP Tweetment

As part of an ongoing census of the birds of Trinity College, we surveyed their diversity just outside our door.

Authors

Trinity College Zoology Students

Photo Credit

Trinity College Zoology Students

17/05/201317/05/2013

We need Tarzan to fill the gaps!

Nature News published a new post about our origins. It’s promoting Stevens et al’s 2013 paper that published the description from two new granddads/grandmas in our already complicated family tree. These guys, Nsungwepithecus and Rukwapithecus (it’s not that hard to pronounce, try it) are considered by Stevens and his team as the oldest crown Catarrhines – [Google translate palaeo-primatish to English: “as closely related as the ancestors of you and your cousin the proboscis monkey (we all knew there were some facial similarities!)”]. Technically speaking, these fossil discoveries pushed the origin of modern Catarrhines back from 20 to 25 million years ago, a date which is closer to molecular results (25-30 mya). Astonishing eh? Well it is for me but there’s another reason why I wanted to talk about this paper: gaps.

As many people might know, the fossil record contains some serious lacunas; thick layers of rock containing either very few or no fossils at all. One example mentioned in this paper is the scarcity of fossils from the Oligocene period; very few bones for palaeontologists to gnaw… The Oligocene was, however, a period of massive changes, in climate and all that stuff but also the time when placental mammals evolved from their primitive to modern forms. So the lack of fossils from this time is always frustrating when you want to understand macro-evolutionary patterns. But why have we found so few Oligocene fossils until now? Of the many explanations Stevens et al. suggest that “Possible reasons […] include limited deposits of appropriate age, particularly […] below the equator, complicated by densely vegetated topography in more tropical environments”. And that’s why I find this article so exciting! Traditionally, fossil primates were excavated in deserts or northern latitudes, which is typically where they are fairly rare nowadays! Therefore, I’m happy to see that there is a true effort being made to look for fossils in biodiversity hotspots such as Tarzan’s neighborhood (or the Tanzanian Rukwa Rift Valley in this paper) where these new primates were discovered.

I think one of the most important things to come from this paper is that it’s proof of a real effort to look for the fossils in the true biodiversity hotspots which, I’m sure will lead to far better comprehension of modern mammalian history. These new primates came from Africa but people are also working in Peruvian jungle and interesting new discoveries are not limited to just primates…

Author

Thomas Guillerme: guillert@tcd.ie

Photo credit

wikimedia commons

15/05/2013

Sentenced to death: how not to communicate science

I like to think the purpose of language (poetry excluded) is to convey information. Doing so in science is complicated somewhat by the vocabulary that every field accumulates. But, from my experience, most of this jargon takes the form of nouns and these are easy to explain when necessary. Take the word ‘phylogenetics’ as an example. On first inspection it’s a polysyllabic monster but as a noun it’s easy to define as “the systematic study of organism relationships based on evolutionary similarities and differences.” Simple. And over time this word slots into our vocabulary so we no longer need a definition every time.

The real problems in the language of science communication lurk elsewhere. Neuroscientists declare the self is an illusion but there is always going to be a subject doing science no matter how objective we want it to be. And it is that subject who should do the explaining of his or her work. The complete aversion of scientists to personal pronouns is a disaster for clarity and renders many papers unreadable. There are instances when the passive voice is more suitable but it’s not a case of ‘I showed’ for the humanities and ‘it was shown’ for science.

Lewis Spurgin lists myriad forms of bugbears in communicating science in one of his blog posts. Pretentious writing and clichés are both listed! As he says, so much light has been shed on matters in science that we’ve all gone blind. So rather than eschewing obfuscation and espousing elucidation try to keep it simple stupid (KISS). Despite Will Self’s eloquent defence of obscure words, in science communication, clarity should be our highest priority.

And finally we come to the “funny title: actual title” format (see this blog post). Spurgin reckons scientists prone to this are in need of a colonic irrigation. And with good cause, for having a colon in your title reduces the number of cites you receive.

Author

Adam Kane: kanead@tcd.ie

Photo credit

wikimedia commons

13/05/2013

Monsterology

Monsters and fantastical creatures are integral components of every culture and society. It’s easy to dismiss fantastical beasts such as Cyclopes, unicorns and mermaids as fanciful creations of story tellers with over-active imaginations. While this may be true, there are also often plausible explanations of either extinct or extant animals which could spark such tales. The intriguing pseudoscience of cryptozoology has a long history which is still strong today.

Marauding Cyclopes seem to have been rampant on the islands of mythological Ancient Greece. One of the explanations suggested for the origins of these one-eyed monsters stems from dwarf elephant fossils found on Cyprus. The central nasal cavity for the trunk may have been interpreted as a large single eye socket which could have sparked the legends. Plausible enough but, if true, the elephant origins doesn’t explain why Cyclopes are never depicted with tusks.

Convinced of their existence, Greek writers included unicorn descriptions in natural history rather than mythology writings. Medieval and Renaissance curiosity collections often included fragments of unicorn horns belonging to the real unicorns of the sea, narwhals. Leaving any magical capabilities aside, the existence of a single-horned artiodactyl isn’t that implausible. Pre-historic contact with a giant Eurasian rhinoceros, the Elasmotherium may be one origin of unicorn stories. More recently, the birth of a roe deer with an unusual genetic mutation resulting in a single central horn sparked many “modern day unicorn” stories.

When early explorers ventured beyond the dire “here be monsters” warning on their limited maps, monster sightings were often confirmed rather than dismissed. Christopher Columbus recorded mermaid encounters en route to discovering the New World in 1492. Sea manatees and their penchant for sometimes sitting upright in the water seem to be the most likely explanation for many mermaid stories – although, even allowing for their seaweed hair, given manatees’ rather homely appearance I often wonder why mermaids were always recounted as being so beautiful.

In later years, curious audiences could pay to see their very own mermaid in the scaly and furry flesh. Fiji mermaids comprised of a monkey’s torso sewn onto a fish’s tail were popular in 19^th century sideshows. Although the Victorian public was rather more gullible than their modern day counterparts, it was not long before Fiji mermaids were identified as a hoax. Such trickery set a precedent which created difficulties when it came to scientific acceptance of seemingly fantastical creatures. In his excellent Life Stories series, David Attenborough recounts the scepticism with which European academics reacted to duck billed platypus specimens shipped over from Australia. Surely a creature with the beak of a duck, webbed feet and a non-descript hairy torso must be a hoax of taxonomic trickery? Sometimes real world animals are far more fantastical than any mythical beasts.

In our genomic age, the study and “proof” of mythical creatures has developed far beyond the amateur status of sewing body parts together. Recently, the Sasquatch genome project has sequenced and published big foot’s genome. The mitochondrial DNA has 100% homology with humans (I wonder why??) while the complete genome is a “mosaic of novel primate and human sequence”. Rejected by the journal of cryptozoology the results are published in a newly founded “peer reviewed” journal with the article only available for purchase and, curiously, remains largely unseen by anyone other than the study’s authors…

Whether based on grains of truth or pure fantasy, the field of monsterology remains strong today. I’m sure the Victorian mermaid stitchers are looking down on their Sasquatch geneticist descendants with pride.

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credit

wikimedia commons

10/05/2013

Surviving experiments

Having just come through a particularly long and intense experiment (relatively unscathed) I thought I’d contribute some of the things I’ve learned and advice I’d give to other poor souls embarking on the exciting and terrifying world of empirical science.

1. Be organized!

I know this is a bit of a cliché but taking the time to work out exactly how much of everything you need, gather your chemicals, buying the labels etc.- it all pays off. Try, if you can, to run a number of pilots to iron out any blaring errors, work out difficult techniques and get familiar with how your system works. The absolute worst thing is to discover three days into an experiment that something isn’t working and you have to start all over again when you could have dealt with it weeks before.

2. Know your stats!

Another thing that I feel is really important and not always practiced or appreciated enough is to know what analysis you are intending to do with your results before you start. Understanding how you will analyse it makes a huge difference to the way and the efficiency with which you collect your data. Too many people don’t think about this in advance and the run into trouble once it comes to looking at their data. Knowing what you want from your data makes it a lot easier and straightforward to collect. It is also a lot more rewarding once you finish.

3. Accept you will have no life outside of work for the duration and share this fact

Realising this early is a big advantage. Warning friends and family in advance that you have time points that mean you can’t meet them in the pub, go for lunches or go away for the weekend saves frustration all round- they don’t think you are blowing them off and you don’t get that renewed sense of disappointment and questioning of “why am I doing this!?” every time you turn down an invitation for something more fun than looking down a microscope for 8 hours. It also saves boring them with your ‘hilarious’ “you’ll never guess what happened to me today? I held the pipette upside down!” stories that only you can appreciate right now, being the only thing to have happened to you all week.

4. Choose your listening and viewing carefully

Chances are you will be spending a lot of time alone and thus you will be turning to media for some company. I have a couple of pieces of advice about this. The first would be to not just rely on music. Singing along is fun for a while but the chances of a melancholic ballad coming on, or your dancing resulting in you knocking over bottles of liquid are quite high. Music all day every day for weeks also doesn’t do too much to pass the time. Chat shows or podcasts are great as you can let your brain engage they really make the time fly. I would also say to try and listen to a program that has the news on it so you remain somewhat in touch with the world. It is also a way of gaining perspective! A side note on TV as well, if you have late night time points, try to avoid too many murder mystery shows- leaves for an uncomfortable night alone in the dark lab in a creaking building!!

5. Make and effort to talk to people (and not just your equipment)

You can quickly cut yourself off from other people and goings on during your experiment and making an effort to go to coffee or pausing for a chat really can be the difference between going completely insane and being merely a little “frazzled”.

6. You’re probably a control freak- don’t panic if things don’t go exactly to plan

I imagine most people that have chosen to go down the empirical route have done so because underneath it all (or on surface!) you are somewhat of a control freak. You want to have power over your system, how it is designed and the kind of data you are going to generate. This is great but what it also means is that dealing with changes or mishaps can be hard. Most of the time these are things that can easily be adapted or fixed, so try not to cry when one thing goes slightly differently to how you had thought it would. Also, don’t count down the days. Take this from me, yes it is a comfort when you reach the last 2-3 days of the experiment but it isn’t much comfort waking up and saying “only 12 days left”. Definitely makes getting up harder!

7. Try to make it fun/pretty!

Experiments can be long, they can be tedious and they are exhausting. So why not do little things to make them just a little more fun and rewarding. Whether it is using one of your non-measuring moments to run and get your favourite coffee, buying sparkly labels and coloured beads to liven up your microcosms, or giving your equipment interesting names. These are all tiny changes that just might make coming into the lab that little bit brighter!

8. Embrace the insanity

If you are doing a long and time consuming experiment by yourself, you will go crazy. It is a simple truth. You reach a point where tedium meets stress meets exhaustion, and they seem to sum to delirium. However, embrace it, let yourself dance to that song when it comes on the radio while you’re pipetting, not chastise yourself too much for talking to the equipment (though see tip 4!) and remember that, in science, a little crazy is expected, even endearing. The mad scientist is already a thing, so you clearly aren’t going to ruin the rep.

9. Be prepared for the come down

This is kind of a strange one, but I think one of the more important ones. Your experiment will end (even if it doesn’t feel like it!). When it does, you need to remember that life is waiting for you again. I think it is a bit like finishing that first exam, it’s finally over and you’re delighted, but then there’s tomorrow to study for. Suddenly you need to make it up to friends, your emails, and your data. Try and prepare for this towards the end of your experiment: Glance at those unopened emails, file all those unread papers, sneak a brief peek at your diary beyond the page marked “end of experiment” circled a thousand times in red pen. This will make the day after the end of your experiment a little less of a shock!

10. Remember you are doing SCIENCE

The last thing and most important of all: Smile and remember, you’re doing that magical thing called science!! However tedious and time consuming, it’s amazing and exciting and you love it!!

Author

Deirdre McClean: mccleadm[at]tcd.ie

Photo credit

wikimedia commons