Dinosaurs are useless if they don’t go in trees!

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I’d like to ask the question many paleontologists have to face when they (foolishly) venture out of their museum storage: “So you’re studying fossils right? But what will that bring to the people? A cure for AIDS?”. There are many possible answers from a punch in the face to more mature responses. But I was recently asking myself the question from a biologist’s point of view: “What can biologists really do with the fossil record?”. Well obviously, we can use it to recreate and understand the history of our planet (like in Nature last week) or to do use some nice methods in trying to understand ancient ecosystems. People even might feel lyrical and do some serious work on paleo-poetry! But all of these guys are paleontologists right? They live in their museums and only go out for a movie once every 10 years… How about the other biologists?

Think about it, when ever you’re studying any organism, it is obvious (thanks to this bearded ape) that they had a 3.5 billion year history behind them. Ignoring that might lead to a misunderstanding? As an example, I’d like to use my favorite PhD-presentation example: the crocodiles. When we talk about crocodiles, we automatically think about the few species of big lizard that live in rivers in the tropical/sub-tropical latitudes. But, after a quick look at the history of our planet, the only description that is more or less correct is “lizard” (archosaurians to be more precise). Crocodiles are composed of many species (8 genera today – soon to be 6 – but >70 in prehistoric times) that lived in rivers as much as in the sea, on the ground or even sometimes in trees and in tropical to temperate climates (remains of crocs were found in Normandy – France).

Well maybe that’s just because of this group. But if you think about it, many other groups have ecological or evolutionary features that becomes truly astonishing once you take into account their full history. For my PhD I decided, with Natalie, to look at this fun fact (life existed before yesterday and the people studying it don’t always focus on dinosaurs) through primates. My idea is to combine extant data based on DNA with extinct data based on morphology to have an integrative tree of all primate history. I agree that this sounds a bit too easy and naive, (the method is a bit more complex) and I’ll probably end up with something more humble. However I think the primates can be a good example to illustrate the point about the hidden diversity among extinct groups. The primate fossils are not dramatically different than the extant once (unlike crocs, there were no pelagic primates) but they still show some really interesting features, for the macroecology side, combined extant and extinct primates show massive variation in body mass in some groups (lemurs) but very few variations in others (tarsiers). Or on the macroevolution side, such an integrative tree could provide some further understanding to the old debate of primate origins! Well at least I hope so. For now I’m just comfortable with eating some burgers with a diet coke and a gun in a pickup truck while I’m scanning some primates in the Smithsonian Institution in Washington DC.

Author
Thomas Guillerme: guillert[at]tcd.ie
Photo credit
Scott Hartman
http://www.skeletaldrawing.com/

Tyre Pressure

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I’ve recently been spending a lot of time working with undergraduate students and marking their work and much of it has been on the subject of evolution and natural selection.  This can be a difficult topic to clarify in the mind of younger students and it’s often difficult to recall specific examples which can be easily explained. Usually you have to come up with some hypothetical situation whereby some selection pressure drives a population towards evolutionary change. A newly published study in Current Biology by Brown and Brown however provides a beautiful (and more importantly brief) example of evolution and natural selection at work.

They have been studying populations of cliff swallows (Petrochelidon pyrrhonota) in Nebraska for almost thirty years, attempting to evaluate the costs and benefits of group living in these highly social birds. In an interview with John Dankosky lead author Charles brown explains how his habit of checking road killed birds for rings (or bands, as they are called in the US) led to an intriguing discovery. Firstly they noticed that over the years fewer and fewer birds were being killed on the roads (Figure 1), but also that these road killed birds tended to have longer wing lengths compared to individuals of the general population.

Figure 1. Change in wing length and number of road killed swallows (From Brown and Brown 2013).
Figure 1. Change in wing length and number of road killed swallows (From Brown and Brown 2013).

So if you are a cliff swallow why does having a longer wing make you more likely to be run over by a car? Well it all comes down to the angle of escape. Birds with shorter more rounded wings are able to take off more vertically compared to individuals with longer more pointed wings, essentially shorter winged birds can get out of the way of oncoming traffic more quickly. It seems that this selection pressure from vehicles has been driving (I make no apology for the pun) the evolution of shorter wings in this population of cliff swallows.

Cliff swallows are migratory birds, travelling from South to North America annually and longer more pointed wings are generally seen as an advantage when it comes to long distance flight. Therefore it seems that the shorter winged individuals may pay an energetic cost compared to their longer winged conspecifics, but this cost may be outweighed by the benefit of being able to avoid traffic. Whatever the case may be I think this study provides a nice example of selection pressures steering morphological adaptations along the road to survival. Next time a student needs clarification on this I’ll remember, tyre pressure.

Author

Keith McMahon: mcmahok[at]tcd.ie

Photo credit

Tommie Kelly (www.tommiekelly.com)

Bees and biofuels….what’s the buzz?

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As oil prices sore and the future of world energy is uncertain, there is rising demand for alternatives to fossil fuels. From solar energy to wind to algae fuel and biodigestion, the alternatives are numerous. One alternative that has received substantial media attention is the use of bioenergy which involves the production of energy from crops including maize, sugarcane, elephant grass and oilseed rape which are grown specifically for energy purposes.

However, the debate over bioenergy crops is often heated. Do they compete with food crops and therefore increase prices in an already stretched market? Do bioenergy crops result in the destruction of tropical rainforest to clear new areas for farmland? And are bioenergy crops even carbon neutral to begin with?

One debate that has been investigated by researchers in Trinity as part of the Simbiosys project is whether bioenergy crops can have impacts on biodiversity – the animals and plants that live on and in farmland. Not only are these animals and plants an important part of our heritage, but they are the pollinators of our food crops, the insects that control agricultural pests and the organisms that help provide us with clean water and air. With two-thirds of Irelands land area used for farming, any changes in farming practice are likely to have knock-on impacts on biodiversity.

A study recently published in the Journal of Applied Ecology investigated how growing bioenergy crops impacts the bees and other pollinating insects that pollinate wild flowers, apples, berries, oilseed rape, clover and many other crops here in Ireland (in fact pollinators are required for approximately 1/3 of all the food we eat). It was found that although different types of insect responded differently, there were no decreases of pollinators in bioenergy crop fields in comparison to their conventional farming alternative. And for some pollinator groups such as the small solitary bees, the introduction of small amounts of different crops into agricultural areas may actually be beneficial.

However, bioenergy crops did not provide the stable nesting conditions needed for pollinators; almost all bumblebees chose to nest in the field margins and hedgerows surrounding the fields. Field margins and hedgerows also provided habitat for large numbers of other insects. The study concluded that small amounts of bioenergy production on existing farmland may provide a diversity of habitats for pollinating insects, but that changes in levels of production in the future may have different effects. Hedgerows and field margins should also be maintained during bioenergy production as they are important nesting and forage sites for pollinating insects.

Although bioenergy crops in their current form seem like good news for bees, the future may be less certain. Growing these crops over larger areas rather than in individual fields, or the replacement of forests or meadows rather than existing arable (tilled) land, may have very different effects. With EU targets of 20% energy from renewable sources by 2020, and bioenergy incentives for farmers, we can expect further changes in this developing sector over the next few years.

Author

stanleyd[at]@tcd.ie

Photo credit

Dara Stanley

Morphological convergence and disparity in Malagasy tenrecs

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I wish to register a complaint…” the first six months of my PhD have passed by far too quickly. As the date of departure for my first major data collection trip looms, I’m navigating the exciting but unnerving transition from the planning to action stages of my project. Fortunately the members of NERD club were on hand to very kindly listen to my ramblings and provide excellent ideas to add to and modify my research.

Here’s the plan so far…

Evolutionary studies have long-been concerned with understanding patterns of variation in morphological diversity. Two aspects of morphological variation which attract particular interest are convergence – the independent evolution of similar morphologies in phylogenetically distant species – and disparity –the range or significance of morphology in a given sample of organisms.

Morphological variation among tenrecs is particularly interesting – they appear to be both disparate from each other and convergent with other species such as hedgehogs, shrews, moles and otters. However, previous studies have neither quantified the degree of convergence or disparity among tenrecs nor attempted to identify reasons for the occurrence of these patterns. My aim is to fill these significant gaps in our understanding of the evolution of such a fascinating mammalian group.

I work with morphometric data compiled from museum collections of tenrecs and the mammals which they convergently resemble (my data collection involves traveling to museums in London, Washington DC, New York and Boston – oh the trials of PhD life!) I use calipers to take linear measurements and also photograph the species’ skulls and limbs. I use geometric morphometric techniques (this article is a great introduction to the murky world of morphometrics) to statistically analyse the degree of morphological (dis)similarity among tenrecs and other species.

I will plot the morphometric data from my species in a “morphospace”, something similar to Brusatte et al.’s 2008 paper on dinosaur morphology. This graphical interpretation will be useful for measuring both convergence among tenrecs and other species and disparity within tenrecs.

In morphospace plots, morphologically similar species sit closer together than dissimilar species. However, from a convergent evolution perspective these patterns are only interesting if morphologically close species are also phylogenetically distant. I will combine and modify existing approaches (e.g. Stayton 2008 and Muschick et al., 2012) to  quantify the amount of convergence among tenrecs and other species and also determine whether tenrecs have evolved a higher degree of convergence than expected by random chance. Similarly, if tenrecs are significantly disparate from each other I expect that the range and variance of their morphological variation will be both greater than random evolution models and also significantly different from their nearest sister taxa, the Golden Moles (e.g. Harmon et al., 2003).

Many texts claim that convergent phenotypes evolve in animals that fill similar ecological niches. However, morphological and ecological convergences don’t necessarily go hand in hand so, while this idea is certainly very plausible in tenrecs, it is important to test the assumption. Fortunately relevant data on physical habitat characteristics, species range maps, life history traits and overlaps with potential competitors and predators are readily available from a range of sources (e.g. PanTheria, LANDSAT and the IUCN) so I can model the ecological similarities among tenrecs and other species. It will be very interesting to determine whether morphological convergence and ecological similarities truly correlate.

So that’s my plan for at least the next six months or so. Interspersed with working in major museum collections while taking a break to tap dance in a parade down Constitution Avenue in Washington DC, I think there are interesting times ahead.

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credits

http://www.digimorph.org/specimens/Hemicentetes_semispinosus/body/

Undead as a dodo?

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While most of the younger generations are familiar with the ideas behind Jurassic Park, they are probably also aware that, despite the best efforts of geneticists, there is no possibility of conjuring up a T. Rex from the fossilised remnants that are on display in museums.

However, there are plans afoot to attempt a similarly ambitious project with species that have disappeared from the earth more recently. These reintroduction programmes, where there are currently no living relatives to repopulate the species, have been termed “de-extinction”. The Long Now Foundation (a private, not-for-profit organisation committed to very long-term thinking about the human population) has conceived a Revive and Restore Project that aims to return some of the planet’s missing biodiversity. Candidate species have already been identified and include; the Passenger Pigeon (US), the Great Auk (Europe), the Dodo (Mauritius),the Huia (New Zealand), the Tasmanian Tiger (Australia) and the Woolly Mammoth (Russia).

Woolly Mammoth Replica in Museum Exhibit
Woolly Mammoth

Genetically-altered (“chimeric”) foster parents can be reprogrammed to produce gametes from other species. So, for example, a chimeric duck can produce chicken sperm cells. Once both male and female chimeric foster parents have been created, they would be able to produce offspring of extinct target species. To some extent, the techniques employed to create chimeric foster parents will be similar to techniques already used in cloning. While those techniques have yet to be perfected, scientists with The Long Now Foundation are confident that they will be.

Great Auk
Great Auk

It seems likely that the Passenger Pigeon will be selected as the first species for de-extinction, because recent phylogenetic work has identified important genetic sequence information, as well as its nearest extant relatives (Johnson et al. 2010). However, it is unlikely that laboratory work will begin on the de-extinction immediately; the ethical and ecological debates surrounding these issues are likely to be protracted.

But if de-extinction can work and the technology is embraced as an important ecological restoration technique, what incredible venues the zoos of tomorrow might be. They could become the places where you go to see the first representatives of a species, rather than the last.

Author

David J Kelly: djkelly[at]tcd.ie

Photo credit

http://true-wildlife.blogspot.ie/2011/04/woolly-mammoth.html

wikimedia commons

Chronicle of a death foreseen

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Why did Neanderthals go extinct while humans prospered? There are volumes full of speculations into the decline and fall of our burly cousin who last walked the Earth 30,000 years ago. Climate change may have reduced the large herbivores on which they depended for food. Humans may have inadvertently spread lethal diseases to them when we first came into contact. Perhaps the most sinister hypothesis is that we extirpated them in an ancient act of genocide (/speciescide?).

Researchers at Oxford now argue that Neanderthal orbit size gives us an insight into the reason for their downfall. They reason that, as Neanderthals had relatively larger eyes than humans, more of their brain was dedicated to visual systems. This was an adaptation to their habitats in the higher latitudes where light conditions were poorer. This came at a cost though because the evolved brain can’t be a master of all trades, there must be some tradeoff. In this case the authors propose that the Neanderthals suffered a reduction in their cognitive abilities.  This was significant because it meant that your average Neanderthal could deal with fewer social partners than a comparable human.

The impacts of this in the authors’ words, “First, assuming similar densities, the area covered by the Neanderthals’ extended communities would have been smaller than those of [humans]. Consequently, the Neanderthals’ ability to trade for exotic resources and artefacts would have been reduced, as would their capacity to gain access to foraging areas sufficiently distant to be unaffected by local scarcity. Furthermore, their ability to acquire and conserve innovations may have been limited as a result, and they may have been more vulnerable to demographic fluctuations, causing local population extinctions.”

But this proposal hasn’t gone unchallenged. Anthropologist Trenton Holliday says that by ignoring the relatively larger faces of Neanderthals the inferred larger visual brain region is mistaken. Another criticism comes from Virginia Hughes over at the Only Human blog. She points out that brains aren’t perfectly modular. So by comparing these idealised modules across species isn’t 100% informative. Perhaps Neanderthal brains were set up in a different way to process social information.

I think the visual system-cognition trade-off is something that could be easily explored in extant fauna. Think of related species that differ in latitude et voila a confirmatory or dissenting paper awaits.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons

Your days are numbered

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Last weekend journalist Rod Liddle applauded the efforts of two scientists who wrote a primer for the lay public on physics. His applause stopped when it came to the content though. The problem for him was the quantity of maths the authors used to get their point across. Liddle wrote “By the time we got onto calculus and derivatives I had long since raided the wine rack and things stopped making sense altogether.” But calculus is an integral part of the Leaving Certificate maths curriculum in Ireland and A levels in the UK so why should an educated man find it so intractable? Well, for one, maths is often taught in the abstract.

Of course many of us struggle with the abstract world of maths so this isn’t restricted to Rod Liddle.  And I realise that not everyone can be a master of all trades. The trouble is, maths is damn useful, and in science it’s indispensable. Look at how Eugene Wigner spoke of the ‘Unreasonable Effectiveness of Mathematics in the Natural Sciences.

In secondary school and throughout university I thought biology was almost a maths free science. How wrong I was. If you ignore the quantitative part of biology you miss a wealth of literature and hamper your understanding of the subject. Without statistics much of biology would be stamp collecting. So it’s worrying that a maths-phobia has infected biologists. Look at this study showing that as the number of equations in a biology paper increases the number of cites it gets goes down. There even seems to be a split in the biological community, the theoreticians on one side and the empiricists on the other.

Back in 1959 the chemist C.P. Snow gave a Rede Lecture in which he decried the split between the sciences and the humanities. He called this ‘The Two Cultures‘. I don’t think we’ve bridged that gap. But I’d hope that biologists can improve the way they communicate with one another. Every effort should be made to make a scientific paper as clear as possible.

This will have to come from both sides. Those quantitative minds will have to make it clearer what they’re talking about. I suggest using in-text drop down boxes to make every step explicit as the number of equations ratchets up. This shouldn’t be a problem as we move away from paper publications and use all of the tools the digital age affords us.

But there is an onus on the rest of us to up-skill. Fortunately this has never been easier. A large proportion of MOOCs are mathematically themed and sites like the Khan Academy are a fantastic resource. A real boon of these courses is they afford anonymity, so you can safely check out logarithm identities without embarrassment.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons

Geese vs. Cyclists

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From October onwards, when most of our resident wildlife is battening down the hatches to endure the impending bleak winter months, flocks of Brent Geese are very welcome visitors to Ireland. Their arduous journey to our shores is impressive for both its distance (approximately 3,000km from Arctic Canada) and the route taken: long-distance sea voyages punctuated by stop-overs in Greenland and Iceland before they reach Ireland. The necessity to escape harsh Arctic winters is very understandable. What’s not clear is why Brent geese undertake Atlantic crossings instead of following other geese species that journey south across the American continent. Whatever twist of evolutionary fate is responsible, there’s no doubt that we are lucky to receive annual visits from such intrepid voyagers.

I’m sure many Dublin residents would agree that sharing seaside walks with companiable small family groups of geese or witnessing one of the chattering fly-overs of a large flock undoubtedly brighten up an otherwise bleak winter’s day. However, a recent Irish Times article identified Brent Geese as the enemies of an unlikely foe; urban cyclists.

For more than 10 years, the S2S group has campaigned to create a continuous cycleway for 22km around Dublin Bay, running from Sandycove on the south side to Sutton on the north side which, if completed, would be Europe’s longest seafront promenade and urban cycle-path. The plan would be a great amenity for both recreational and commuter cyclists – you only have to travel along the coast road from Fairview to Howth to witness the popularity of the existing cycle path along the black banks. Just 8 km of the route remain to be completed, mostly on the south side and a single 4km stretch from Sandymount to Blackrock is particularly controversial.

The proposed route would cut through EU protected bird habitats and, in particular, affect an area of eel grass consumed by Brent Geese. The National Parks and Wildlife Service (NPWS) is also concerned about the impact of the cycle way on other bird species which reside in protected areas in Booterstown.

While I’m often wary of articles alluding to stereotypical views of “conservation hippies” thwarting sensible developments, in this case I have to agree with councillor Barry Ward that there must be a solution which “inconveniences rather than displaces” the geese. No development affecting protected habitats should be undertaken lightly. In particular, since the majority of Brent geese overwinter at just 10 sites, Birdwatch Ireland lists their conservation status as “medium concern”. However, with their current population seemingly in good health and the plethora of suitable habitat which Dublin Bay has to offer, it seems unlikely that an 8 metre wide seafront path would have a major impact on the goose population.

I’m well aware that if every development took the attitude of “there’s plenty of habitat elsewhere” then there would be no protected areas left.  In addition, I must admit my vested interest in seeing the cyclepath completed – I’m a recreational (i.e. fair weather!) cyclist and live in Sutton so the availability of 22km of off-road cycling on my doorstep is a very attractive prospect. However, if you observe the behaviour of geese along the existing cycleway they seem to be remarkably unperturbed by adjacent human activity and continue to forage just below the boundary wall. Surely the same coexistent relationship between cyclists and geese could be forged south of the Liffey?

Despite including the S2S cycleway as part of their development plan councillor Barry Ward argues that management of the Dún Laoghaire Rathdown county council seems to be reluctant to develop the cycleway. Beyond the legitimate concern that the proposed cycleway would pass through a protected area, there seems to be no specific predictions or estimations that the development would have an adverse effect on the geese.  Rather than an issue of cyclist vs. geese, perhaps this story is really a case of scape geese taking the blame for a council’s reluctance or inability to fund and implement a new development?

Author

Sive Finlay sfinlay[at]tcd.ie

Photo credit

wikimedia commons

Comedy science

Last Wednesday a bunch of us (thanks to @nhcooper123 for organising) went to see Robin Ince @robinince perform his stand-up comedy science show The Importance of Being Interested at the Science Gallery. His shows are a unique blend of education and humour, combining a whistle-stop tour of the world of science with hilarious anecdotes, all the while vehemently challenging the doubters and the nay-sayers.

I found his show immensely inspiring, and I have to admit that I am normally bored by pop-sci outside of the relative academic safety of my office. I took so much from the show, but I think it boils down to these three points:

  1. The world is big and wide, and fully of wonder. I kind of know this. Its pretty much the reason why I’m a scientist, but Robin has a wonderful charm and ability to find all the really cool stories and point out the best bits, even when showing you something you already know. Be in awe of the world around you.
  2. Don’t sit back and swallow the crap. He would doggedly challenge the stance of anti-science types or the science ignorers. He took the anti-vaccine brigade to task, mocked homeopathy and challenged the religious devout. Recently, I have found myself sitting on my hands, and shoving food in my mouth at parties so as to avoid getting drawn in to discussions – well, arguments really about such matters. I have been taking a pacifist’s approach that in retrospect is cowardly and does a dis-service to science and the work of all my colleagues and my own. But no more. Bolshy grumpy argumentative Andrew is back (just ask my colleagues). I’m not sure my wife will thank @robinince but apparently he suffers from foot-in-mouth too. Be true to your convictions.
  3. Don’t be shy. His style is mad, frenetic, at times all over the place, but always entertaining. Its all too easy to retreat into your shell when you present in public. People like Robin remind you that an entertaining style will hold your attention no matter how many beers you sank during the interval. Equally, you don’t be yourself when on stage. You can put on a show, be something different, whatever works to entertain. Lecturing is an act. Tell funny stories – why you will get poo on your finger if you stick it up your bum for instance. Swear at least occasionally (this is one of my tricks and usually gets a giggle and wakes up those in torpor). Be fun, be mad, be witty and be entertaining.

If at all you like science, one of his shows is a must see. Hopefully this inspiration lasts. If not, I will just have to go see his show again.

Author

Andrew Jackson: a.jackson[at]tcd.ie

Photo credit

wikimedia commons

Fly Away Home

The University of Exeter team visited Ireland this week as part of their ongoing investigation into the biology of the Brent Goose. This species has a remarkable migration, spanning from Northern Canada to Western Europe. The team collects DNA samples, blood for stable isotope analysis and various morphometric and behavioural data. We joined them on Wednesday to help out.

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Step 1. Man the net
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Step 2. Recover your goose
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Step 3. Measure your goose
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Step 4. Admire your goose  
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Step 5. Release the geese

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

Adam Kane