Let the games begin!



We the blog declare that a month of games will commence from tomorrow. The aim is to achieve the most hits for a blog post in a day. The prize will be worth that of a King’s Ransom and will be revealed in good time. Cry havoc, and let slip the blogs of war!


Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons





Intelligent Design: Part One – a brief explanation and history


Trinity College Theological Society recently held a talk by Dr Alistair Noble titled ‘A Scientific Case for Intelligent Design’ which I attended as, possibly, the only biologist in the room. It was a fascinating, if deeply frustrating, experience. Before I get into the details of the talk, a brief explanation of intelligent design may be necessary. . .

Intelligent design (ID) is the ‘theory’ that certain features of the universe, including life, are best explained by invoking a creator. I put ‘theory’ in quotes because in a scientific theory is a very particular beast. It must have both explanatory and predictive powers. For example, the theory of evolution by natural selection explains how life evolved and can also be used to make predications about life that can be tested. The ‘theory’ of intelligent design has little explanatory power (“the designer did it”) and makes no predictions. As such, it is held with little esteem within the scientific community.

Outside the scientific community, however, there are some who hold ID in very high esteem. They think that it is a credible scientific theory and there have been many attempts, particularly in the U.S., to have ID taught in schools as a counter to evolution. This is deeply worrying to those who care about scientific literacy but has to be tackled carefully.

The reason for such caution is that ID is most loudly promoted by religious groups who feel that the theory of evolution is anathema to their beliefs and as such must be countered. In the past they countered with Creationism, but in recent years they have tried to remove the explicit religious overtones of Creationism, removing God, replacing him with an unspecified ‘designer’ and calling the new theory ‘intelligent design’. Thus the debate around ID is not just a scientific debate but is also a religious debate involving deeply held personal beliefs.

I hold the opinion that your personal beliefs are yours, and are no concern of mine, but when you try and mess with science, well, that’s another story! I went to the talk as I was curious to hear the scientific evidence for ID. Would it persuade me that there was a case for ID? . . .



Photo credit

wikimedia commons

Good-bye Guinea worm?


The media is all abuzz about the Carter Centre’s recent announcement that 542 cases of guinea worm infection were reported in 2012. That is a remarkable achievement, considering that 3.5million cases where the reported when the Carter Centre began their eradication programme in 1986. The guinea worm (Dracunculus medinensis) is a particularly gruesome parasitic nematode that causes painful and debilitating disease. It is one species no one will be too sorry to see go. Well no one except the folks at the (tongue in cheek) Save the Guinea worm Foundation.

Perversely, considering our track record of causing extinctions, actually trying to get rid of a species can be extremely difficult. Targeted eradication of disease in humans has been successful only once before, with small pox. That required a massive and expensive vaccination programme and it is unlikely that the mandatory aspect of the vaccines would be tolerated today. However, helminths are a different beastie altogether.  Helminths (parasitic worms) differ from pathogens in that, with a few exceptions, they don’t multiply within human hosts or have direct transmission. Helminths require a period of passage through the environment, either as infectious eggs or through other intermediate hosts. The guinea worm life cycle involves water fleas (Cyclopidae) as intermediate hosts.  Water containing infected water fleas is drunk and the parasites are released. After about a year of maturation, females emerge via a painful skin blister, which erupts on contact with water, releasing thousands of larvae ready to continue the cycle.

The peculiarities of the life cycle meant the eradication programme was successful, not though vaccination or medication, but through changing people’s behaviour in the key areas of transmission and infection.  To prevent infection people were taught about the need to filter drinking water, particularly standing water where cyclops abound. The burning sensation caused by the female worm emerging meant people often cooled the blister in a nearby pond, usually the same the one that supplied drinking water.  By educating about the link between this behaviour and infected ponds, transmission of the larval stages was successfully reduced.

Of course, various other aspects of the guinea worm life cycle played a part. Cyclops is a relative large (1mm) so filtering material could be made and supplied cheaply. They are also immobile; once an infection is eradicated from an area it is easier to keep it out than in diseases like malaria. Unlike helminths that release eggs and larvae through the intestinal tract, people shedding guinea worm infectious stages are much more likely to be identified quickly.

One important factor influencing the success of small pox eradication was that the virus had no hosts other than humans. There is no wildlife reservoir from which the disease may re-emerge. Guinea worms on the other hand have been found in cats, dogs and cattle, though none appear to act as a reservoir for human infection. It may, therefore, be more correct to speak of elimination of human guinea worm infections rather than total eradication of the species. Save The Guinea Worm Foundation will be pleased.



Photo credit

wikimedia commons

Punch it in the face! Coping with cuteness…


Why is it that the first things that happen upon seeing a pudgy baby panda, fluffy penguin or tumbling kitten are usually utterances of “squeezing it”, “eating it” or “smushing it”!?

We’ve been talking quite a bit about ‘cuteness’ in the department for a while now; what makes an animal cute, animals exploiting that inbuilt ‘cuteness measure’ we seem to have (*cough* Cats *cough*!!), there was even talk of making a ‘cuteness coefficient’ to see how closely mammals and birds illicit the same responses. While we agreed that the degree of cuteness is definitely a personal thing, there is certainly a general idea that we as humans all seem to hold as universally cute. These usually include a host of wide-eyed, round headed, roly-poly baby animals. There are a number of evolutionary theories behind why we find animals cute (Jerry Coyne’s blog has a nice summary), but what we didn’t discuss, and something which only occurred to me recently upon reading about a new study, was that, not only are our perceptions of cuteness relatively universal (hence the overwhelming number of kittens on the internet), but that so were our reactions, though not in the way you would intuitively expect.

Why do we seem to have an overly aggressive response to cute and fluffy animals? The reaction of most people to a big-eyed bundle of adorableness is not “ I want to hold you and keep you safe forever” or “ I want to coo at you from a distance” but instead expressions of violence and threats of immediate harm! People are compelled to express violent urges on encountering what seems to be insurmountable cuteness. Many people in fact can’t even keep still when something cute comes along- teeth are clenched and hands struggle to fight the “must squish it” impulse.

A recent study presented in New Orleans by the Society for Personality and Social Psychology decided to look deeper into this phenomenon and further, to see whether these verbal expressions of feeling were actually translated into actions. To do this they selected 3 groups of people, and, telling them that this was a study about motor activity, they handed out sheets of bubble wrap to each person. They were free to pop as many or few bubbles as they felt while watching one of three slideshows. One was of funny animals (e.g. dog with its head out of the window), another of serious or plain animals photos and the third of cute animals. Those who watched the cute animal slideshow popped an average of 1/3 more bubbles over the other groups. What this demonstrates is a potential for those violent utterances to be translated into actions: think of an old aunt squeezing her nephews cheeks or an over zealous toddler hugging a cat until it can’t breathe.

The researchers think that, far from people actually wanting to fry up and devour a basket of puppies, these expressions are a way of coping with the situation: “I can’t handle it”, “too cute”, “emotional overload… need an output” sort of thing. The three hypotheses they put forward for this were:

  1. We have an impulse to care for what we perceive as cute for evolutionary reasons. The problem is that not everything we see we can care for (particularly if it is a photo!) and as such we get frustrated.
  2. Too much love: The yearning to care is so strong and we simply get carried away (much like the aforementioned over zealous toddler).
  3. It is simply an emotional overload that we don’t know how to deal with so act on some form of displacement activity.


So it seems, for whatever reason, when people complain about the number of sickly cute animals on the internet or the superfluous efforts put into conservation for the panda rather than the pig-nosed frog in the context of how much they want to “just punch them the face”, what they are really saying is that they cannot handle the emotional overload induced by those animals and that they want to express their love.


Deirdre McClean: mccleadm[at]tcd.ie

Photo credit

wikimedia commons

Men are from Earth and women are from Earth


We love to explore and our adventures into outer space represent the acme of our derring-do. But when we leave our cozy planet we put an awful lot of stress on our minds and bodies. The billions of years of evolutionary pressures exerted on our ancestors all took place within the confines of Earth so a sudden dose of zero gravity is completely alien to us.

Some of the effects of space travel will give even those among you with the right stuff cause for pause.

There are the obvious perils like the terrifying oxygen-less vacuum of space but other, less obvious, afflictions abound.

Okay, so our skeletal system allows us to saunter around this planet quite comfortably. The whole point of the system is to provide some structure and locomotory ability against the force of gravity. But remove the pull and the bones start to wither away. There’s no longer any strain for the bones to resist. It happens at quite an alarming rate too. An average (?) astronaut can expect to lose 1% of his bone mass per month due to spaceflight osteopenia.

Still there’s no shortage of people who’d jump at the chance to be a star voyager for a few months.

But with longer flights, like a mission to Mars, there are even more insidious problems to consider. Back in 2010, six astronauts were selected to simulate such a mission (I was rejected for being too tall). They were locked in a room modeled on a spacecraft and given tasks that would be typical of such a journey. The whole ‘trip’ took 520 days and was an effort to better understand what happens to a person during a period of prolonged isolation.

While not quite space madness the six developed a range of symptoms. Chief among them were hypokinesis and disturbed sleep-wake cycles. The authors of the study describing the effects believe that the cause of these problems was a disruption to the circadian rhythms of the people involved. On Earth, we have our 24 hour day with its predictable light and dark cycle. But in space there is no such thing. Subtle changes in light can throw off your internal clock. This would be quite problematic. If one person has changed to a 25 hour day this can destroy the working ability of the team because he’ll find himself sleeping when everyone else is up.

It’s quite frustrating that we don’t have a biological blank slate that can adapt to all conditions. When we blast off from Earth, one thing we don’t leave behind is our evolutionary past.


Adam Kane: kaned[at]tcd.ie

Photo credit

wikimedia commons

Anatomical enablers in the evolution of grasses

Thuarea (a C4 grass in flower)
Thuarea (a C4 grass in flower)
A paper just published in the Proceedings of the National Academy of Sciences USA (including Trevor Hodkinson, Botany, School of Natural Sciences, TCD; Trinity Centre for Biodiversity Research) highlights the role of leaf anatomical change in the evolution of a type of photosynthesis (classified as C4) that has allowed a large group of grass species to dominate warm regions of the world and become important crops such as maize, sorghum and sugarcane. C4 photosynthesis is a series of anatomical and biochemical modifications to the typical C3 pathway that increases the productivity of plants in warm and dry conditions. The C4 trait has evolved over 20 times in grasses, and all origins occurred within one species rich group. Leaf anatomy traits of grasses were quantified and analyzed in an evolutionary framework.


Statistical modeling indicates that C4 evolvability strongly increases when a particular type of anatomy (proportion of vascular bundle sheath) reaches 15%.  A reduction in the distance between the bundle sheaths occurred before the evolution of the C4 grass group but not in other groups of grasses which lack the C4 trait. Therefore, when environmental changes promoted C4 evolution, suitable anatomy was present only in members of this group, explaining the clustering of C4 origins in this group. These results show that key alterations of leaf anatomy facilitated the repeated evolution of one of the most successful physiological innovations in flowering plant history.


Trevor Hodkinson: hodkinst[at]tcd.ie

Photo credit

Trevor Hodkinson

The Perks of Zoology; Field Work in the Greek Islands


One of the many things I love about Zoology is the opportunity to work away from a desk. As an undergraduate I enjoyed field courses and summer projects in the not so exotic wilds of Ireland and Cambridgeshire – great experiences but not quite a match for the glamour of the recent TCD trip to Kenya! Last summer, however, I was fortunate enough to expand my zoological horizons by working as a field assistant in the Greek Islands.

I travelled to the remote island of Folegandros, one of the quieter tourist destinations in the Cyclades, to assist Kate Marshall, a PhD student in Behavioural Ecology at the University of Cambridge (supervised by Dr. Martin Stevens and Professor Nick Davies). Kate’s research focuses on the evolution of morphological and colouration phenotypic divergences in Erhard’s wall lizards (Podarcis erhardii). She is particularly interested in studying the roles of both natural selection (adaptations to avoid predators) and sexual selection (signals to other lizards) in driving the evolution of varied colour patterns in lizard populations on different islands.

Kate is modelling the lizards’ colouration from the perspectives of predators (birds) and conspecifics (other lizards). Some of her early results indicate that P. erhardii populations have evolved colour patterns and behaviours that are locally adapted to different island environments. Dorsal and head colour patterns seem to be well matched to the lizards’ local environments- indicating a possible function in predator avoidance – while the lizards’ sides are brightly coloured and may play roles in conspecific signalling and sexual selection (Fig. 1).

Fig.1: A male of an island subspecies of Erhard’s wall lizard (P.e.mykonensis). The brighter blue colouration along the side of the body, which seems to be involved in conspecific signalling, is clearly visible.
Fig.1: A male of an island subspecies of Erhard’s wall lizard (P.e.mykonensis). The brighter blue colouration along the side of the body, which seems to be involved in conspecific signalling, is clearly visible.

Some of the most enjoyable parts of my time in Greece involved trying out the unusual techniques which form part of Kate’s research methods. For example, I helped her conduct a pilot study to assess whether predator attacks on the lizards might vary in different islands. This involved making 3D lizards out of modelling clay, distributing them across line transects and checking them for signs of predator attacks such as rodent bite marks. The whole process attracted a few curious looks from the locals as we marched through town with boxes of clay lizards! However, these glances were nothing compared to the reactions elicited by our lizard wrangling attempts. Using an extendable fishing rod, dental floss and noose-tying know-how, we patrolled the island’s hiking paths trying to catch unsuspecting sunbathing lizards by slipping the noose around their necks. The technique was successful in some of Kate’s other field sites but unfortunately we had no such luck during my time – just some very confused stares from locals and tourists as we slowly “fished” our way down the mountain side!

I thoroughly enjoyed my time helping out in Greece. The project covers an interesting area of evolutionary biology – studying the often conflicting influences of both natural and sexual selection in driving phenotypic divergences within species. It was also a great learning experience because it gave me an insight into some of the details and challenges involved in planning a PhD before I started my own project. Finally (and perhaps most importantly), it wasn’t all hard work – combining fieldwork with swimming in the clear blue Aegean or afternoons at the beach were just further confirmations that you can’t beat the perks of being a Zoology student!


Sive Finlay: sfinlay[at]tcd.ie

Photo credit

Sive Finlay, K. Marshall

Another piece in the trophic puzzle


The food chain is a concept that many non-biologists are familiar with. Ecologically-speaking, this should be referred to as a food web, because there is rarely one prey species for a given predator or one predator of any given species.

The biochemistry of metabolism and digestion means we can reconstruct the diet of a member of a given food web with some basic information about the stable isotopes in its tissues and the stable isotope values of the available prey. Simply put, “you are what you eat”. Carbon isotopes generally reflect the “where” of the diet and nitrogen isotopes generally indicate the “what”.

This overview omits several complications. Firstly, the calculation of diet requires a “conversion factor” (trophic enrichment factor or TEF) for any given tissue of an animal. Animal metabolisms tend to retain 15N, so consumers have greater 15N:14N ratios than their prey. Secondly, each tissue is likely to have a different TEF, as it is made to perform a different job in the animal. Thirdly, TEFs can only be derived by feeding animals highly controlled diets, ideally a single food for the length of time it takes for the study tissue to be fully replaced. In the case of teeth and bone, this can be months or even years.

As there are relatively few TEFs available for animal species, many ecologists “borrow” TEFs from other species for their calculations. Having derived TEFs for carbon and nitrogen in badger blood serum, a tissue that is completely replaced several times a month, we demonstrated that badger TEFs differ from fox TEFs. This is important, as foxes are similar in size to badgers and have a similar feeding ecology, and ecologists might be tempted to “borrow” fox TEFs to use in badger studies.

So knowing more about the biochemistry of badgers (in the form of TEFs) will allow us to learn more about their diets. This may be of importance to farmers planning biosecurity measures for their farms, as they will be able to learn if badgers are raiding their crops (in the field or in the barn). It will also help identify when badgers are specialising on different foods and potentially allow farmers to minimise contact between badgers and livestock.


David Kelly: djkelly[at]tcd.ie

Nicola Marples

Photo credit

wikimedia commons

Unlocking your potential with the British Ecological Society


At their Annual Meeting in December just gone, the British Ecological Society held a special event for PhD students and Post Docs entitled “Unlocking Your Potential – Keys to a Successful Career in Ecology”. The purpose of the meeting, as you might have guessed, was to provide early career ecologists with advice on how to go about attaining and maintaining a career in the diverse field of ecology. This was not a meeting on how to survive your PhD, although as you can imagine, there were some small tips. The meeting, craftily held in a bar, featured a fantastic panel of speakers from a variety of ecological backgrounds, at various stages of their careers. In attendance were Professor Steve Ellner from Cornell University, Professor Georgina Mace from University College London, Jenny Bright from the RSPB, Paul Craze, editor of Trends in Ecology and Evolution, and Franciska De Vries from Lancaster University.

Each member of the panel effectively summarised how they progressed from studying as an undergraduate to where they are today – in around seven minutes! Each spoke very fondly of their current positions and the paths they had chosen in order to get there. What was most interesting was the diversity of career paths taken after each completed their PhDs. While some walked straight into a Post-Doc, others took more time, struggling to find a Post-Doc available or that they were interested in. Another found great opportunities in filling various short-term university teaching roles and never found the need/want (I can’t say which) to go for a Post-Doc. And another, knowing exactly where they wanted to work, had to volunteer and persist until finally getting their foot in the door with a contract. The diversity of paths taken directly relate to the type of career each speaker aspired to, as well as their personal interests.

Below are the main points I took from all of this, which I think hold relevance for current PhD and Post-Doc students, as well as those further along in their careers. Although it’s not always easy, spend time thinking about where you would like to go next and what you would like to do (i.e. what really interests you). However, remember things won’t always go as planned. Sometimes, no matter how well prepared you are, i.e. with the correct skill sets, good connections and an impressive academic history, there are forces beyond your control, e.g. a dip in the economy, changes in funding practices etc. Of course, other times everything will go exactly as you had planned, if not better! The panel admitted that so much of this progression comes down to luck and the opportunities that present themselves.

In the Q&A that followed, one chap asked a great question – “How do I make my own luck?” The consensus from the panel: by recognising a good opportunity when it comes your way and grabbing it by the… Opportunities will eventually present themselves; you need the ability to differentiate between those that will take you even slightly further in your desired direction and those that won’t. One of the major rewards: being able to go to work and effectively just work on whatever it is that really interests you.


Seán Kelly: kellys17[at]tcd.ie


Photo credit

wikimedia commons

Hey Tree of Life! How’s it growing?


Following the influence of science writers such as S.J. Gould, I always try to look back at the historical perspectives of what I’m studying. These days I’m playing with 3Gb trees so I was delighted by Mindell’s 2013 Systematic Biology publication about the Tree of Life.

The idea of placing species into the so called Tree of Life emerged before the Origin of Species with works such as Augier’s Arbre Botanique (1801) (Fig. 1) and Eichwald’s tree (1829 – possibly inspired by Pallas’s 1766 work) (Fig. 1). But the spreading of such trees began only after publications of Lamarck’s scheme (1809,Fig. 2), Darwin’s famous sketched drawing (1859 – Fig. 3) and Haeckel’s beautiful tree (1866 – Fig. 2). It is only within an evolutionary framework that these representations of the relationships among organisms make sense: the idea of descent with modification.


Figure 1: Augier’s Arbre Botanique (1801) & Eichwald’s tree (1829) – from Mindell 2013 (Fig.1)


Figure 2: Lamarck’s scheme (1809) & Haeckel’s tree (1866) – from Wikimedia Commons


Figure 3: Darwin’s Origin of Species unique figure (1859) – from Wikimedia Commons

From that point, we all know how the story continued; from Darwin’s sketch (Fig. 3) to modern phylogenomics (fig. 4). Our understanding of the Tree of Life progressed from Simpson’s (this one, not this one) cladistic methods for looking at morphological relations among vertebrates, through to the discovery of DNA, the first molecular clock and, eventually, the use of complicated Bayesian stuff. Depictions of the Tree of Life evolved from something like a cypress (a nice, straight tree with Neil Armstrong at the top surrounded by monkeys and mosses and jelly fish near the roots) to a three-rooted shrub full of immense dead branches near the centre. If you look at the figures included in this  blog, the changes in our understanding of the tree are clear: a gradual reduction of anthropocentrism and inclusion of  microscopic organisms.


Figure 4: Tree of Life from David and Alm (2011) – from David and Alm 2011 (Sup. Fig. 15)

So what should we do next? Should we just expand the dataset until we have all the species and all their genome plotted in the Tree of Life? Hopefully there are still lots of less boring things left to do for researchers working in this area today… Two questions are (in my mind) really important to look at: is the Tree of Life only the result of descent  with modification and what should we put in the tree?

For the first question, it appears more and more clear nowadays that the Tree of Life is not really a tree but rather something along the lines of a tree-shaped web. Regarding Archaea and Bacteria alone (the majority of organisms in the tree), it is estimated that at least 81% of their genes have been laterally transferred among lineages at some time in the past. This phenomenon is also becoming increasingly evident among Eukaryotes (even among vertebrates!) and recognition of these events should lead to a more web-shaped “Tree” of Life. Incidentally, it is interesting to note that Batsch recognised this web structure in plants as early as 1802 (Fig. 5).


Figure 5: Batsch’s web of plants (1802) – from Mindell 2013 (Fig.1)

Regarding the second question, asking what can be included in the tree of life comes down to how we determine what is living. I remember one question that a classmates had in my phylogenetic lectures; “What is the out group of the tree of life?” The lecturer had just said that a tree without an out group is not valid. The resulting discussion turned into a really long (and interesting) debate about viruses – the question being whether we should put the viruses in the tree of life? We might define living organisms by entities that can replicate their own DNA. So you could argue that if viruses cannot achieve this independent replication then we should prune them out of our tree. Haha ! But wait, it’s not so easy: although most viruses require host cells for reproduction, so do many other “living” organisms like Richettsia or Chlamydia. In addition, some viruses have many genes involved in DNA replication so how should their self-replication abilities be classed ?

Mindell conclude by quoting Brooks and van Veller (2008): “There are two choices. Do we classify a tree with [lateral transfers], or do we try to classify a [lateral transfer] network? If we wish our classifications to reflect what we think we know about evolution, it seems that we will have to opt for the first alternative.” Does this mean that we should go for a tree shaped web including viruses? Let see how the debate will go on…


Thomas Guillerme : guillert[at]tcd.ie

Photo credits

wikimedia commons

Mindell 2013

David & Alm 2011