Author: EcoEvo@TCD

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What did what to what? Finding causality in chaos.

A new paper has been published in Science by George Sugihara and colleagues, which is an immediate contender for the most insightful paper I’ve ever read. In the paper they outline a new method, which they dub ‘Convergent Cross Mapping’ (CCM), for detecting causality between variables using time series data. Not only does CCM allow for the detection of causality but also its directionality. The method takes us well beyond the previous confines of Granger causality (which requires the assumption that systems are linear, or are showing linear behaviour near an equilibrium), and allows us to tease out causality in systems that show non-linearity and chaos. As examples of possible applications of their method the authors address two classic causality problems:

Predator-prey dynamics of Didinium and Paramecium. The authors show that there is bidirectional causality in this classic predator-prey system, but that top-down control is stronger than bottom up control (i.e. Didinium has a larger effect on the Paramecium population than vice-versa).

Dynamics of Pacific sardines and anchovies. There has been a long-standing debate about the cause of alternating dominance between sardines and anchovies in the Pacific. Some arguing that competition between the species is the driver, while others claim the pattern is caused by differing responses to temperature. The authors weigh in on this debate by showing that, while sardine and anchovy abundance is negatively correlated, this is a mirage as there is no causation in either direction. The authors also unambiguously show that sea surface temperature does causally affect the abundance of both species, indicating that climate is the main driver.

I think this method will be absolutely invaluable to future studies, and for me has already proved its worth from the results the authors present. The videos below are from the supplementary information of the paper and explain the method simply using beautiful illustrations.

watch?v=7ucgQE3SO0o

watch?v=NrFdIz-D2yM

watch?v=rs3gYeZeJcw

Author

Luke McNally: mcnall[at]tcd.ie

Photocredit

Wikimedia commons

 

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Darwin’s insects, Dodo skeletons and macaques with braces

macaque braces

The Natural History museum in Dublin is one of my favourite places in the city. It has a very Victorian feel to it, none of this pandering to the X-box generation, just cabinet upon cabinet of mounted skins and skeletons revealing the diversity of nature. Some of the taxidermy is pretty hilarious and you can see the bullet holes in some of the skeletons, but that adds to the charm of the place!

I did a lot of museum based work during my PhD and absolutely loved using museum collections, so now I have my own students they all have museum collection aspects to their projects (whether they like it or not!). They will be using the collections in the Dublin museum, so today we had a tour behind the scenes of the museum, and a look at the storage areas with one of the curators Nigel Monaghan.

It was awesome! In the space of a few hours we saw insects collected by Darwin during his time on the HMS Beagle, a Dodo skeleton, a macaque skull with orthodontic braces (the original owner was apparently a dentist, though no-one is sure whether the macaque had braces in life or was just used for practice after it died), an entire room full of Irish elk crania and antlers, some wild Irish grass snakes (Ireland historically has no snakes of any kind), a DNA bank for every Cetacean stranded on the Irish coast, a huge selection of bird parts collected from birds that accidentally flew into lighthouses, and probably the funniest interpretation I’ve ever seen of what a guinea pig should look like.

As we went around, many of the things Nigel told us got me thinking about what an under used resource museum collections are. Certainly many people use the big collections in London, Paris, New York and Washington DC, but few of us would think to look in our local museums. For example, Nigel told us that a geneticist did a piece to camera in the museum recently and mentioned how wonderful it was that they had managed to extract Dodo DNA from a specimen in France. They seemed completely unaware of the fact that the Dublin museum has a beautiful Dodo skeleton in its collection. So my message is go out and use your local museum collections (or at least ask the curators if they have what you’re looking for)! They’re wonderful sources of information and inspiration, whether you’re a first year undergraduate student or a tenured professor. Right, now where did I put my calipers…

Author 

Natalie Cooper: ncooper[at]tcd.ie

Photo credit

Natalie Cooper

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“To expect the unexpected shows a thoroughly modern intellect”

I spoke before of how to use mathematics to convey an idea in biology. Here, I’ll take a different tack and discuss a paper in which the author makes his argument with naked English. The author in question is Nicholas Humphrey who in his famous paper ‘The social function of the intellect’ draws a wonderful metaphor of Mother Nature as an economist,

“It is not her habit to tolerate needless extravagance in the animals on her production lines: superfluous capacity is trimmed back, new capacity added only as and when it is needed”.

His metaphor serves as an introduction to the puzzle of the seemingly unnecessarily inflated intellects of some animals, notably humans.

Humphrey questions if such a highly developed intellect is really necessary for invention. The ability to produce tools is generally not a result of deductive reasoning or creative thought but rather follows from aping other individuals or pure trial and error learning. The intellect must have some other function in his estimation and in the end, he proposes that it is as a social glue. The complex interactions that arise out of the social milieu require some serious intellectual horsepower,

“[S]ocial primates are required by the very nature of the system they create and maintain to be calculating beings; they must be able to calculate the consequences of their own behaviour, to calculate the likely behaviour of others, to calculate the balance of advantage and loss – and all this in a context where the evidence on which their calculations are based is ephemeral, ambiguous and liable to change, not least as a consequence of their own actions.”
 

Calculating the consequences of your own behaviour is one thing but understanding that others around you have motivations of their own is a huge leap in understanding. All of this is done without ever having direct access to the subjective thoughts, motives, and desires of another person. Understanding the reasons for understanding is even more impressive and Humphrey’s paper has rightly influenced the theories of scientists since its publication. Most recently a study in the school that mechanistically linked sociality and selection for intelligence.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

Wikimedia commons

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A vision for the 21st century workplace

I feel a bit of a fraud complaining about the discrimination of women in science because in my current job I’m one of four women in a discipline with only nine faculty members, our head of school is female and so is our head of discipline. I also don’t have any children so I haven’t had to deal with the problems that go along with that. However, I’m not blind; I can see there is a problem! I don’t want to re-hash the problems women in science face in this post; particularly as they’ve been so well covered elsewhere (there have been lots of really cool blog posts about this following the recent Moss-Racusin et al. paper in PNAS). Instead I want to think about potential solutions. Continue reading “A vision for the 21st century workplace”

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The plight of the bumble bee; diapause, immunity and parasitic attack

Sphaerularia bombi with an everted uterus.

Bee populations are in severe decline, an alarming and worrying trend when you consider their vital importance as commercial and ecological pollinators. Research and media attention often focuses on afflictions of honeybees such as the Varroa mite and colony collapse disorder. However, parasites are also major contributors to the plight of the bumble bee.

Bumble bee queens spend 6-9 months in diapause, a hibernation-like state which allows them to survive harsh winter weather. My research demonstrated that queens have reduced immune function during this time, leaving them vulnerable to infections and parasitic attack.

Sphaerularia bombi is a common yet poorly studied nematode which is found primarily in the Northern hemisphere, infecting up to 50% of queen bumble bees in some areas. Adult female Sphaerularia present in the soil infect diapausing queens. My project showed that, with their immunological guards down, the queens cannot mount an effective response to invading parasites.

Sphaerularia exerts significant influence on its host after the queens emerge from diapause. The nematodes evert their uterus to a structure 300 times the volume of the rest of their body (see picture above). This enormous uterus releases numerous eggs into the host and also extracts nutrients from the bees.

Sphaerularia castrate the queens so they don’t form new colonies. The parasite also changes queens’ behaviour so they go to sites suitable for diapause even though it’s the wrong time of year. Having released larval stage nematodes into the soil, parasitised queens die while the nematodes are then poised to infect new queens entering diapause.

Sphaerularia clearly has a significant impact on a host species with high ecological and commercial value yet it remains very poorly studied.  In collaboration with research currently being performed by PhD student Joe Colgan (Trinity College Dublin: Supervisor Dr. Mark Brown) and Dr. Jim Carolan (National University of Ireland, Maynooth), my project filled some of the gaps in our understanding of the molecular interactions between host and parasite. One particularly interesting finding was that S.bombi infection seems to change the protein expression in bees, indicating a complex interaction between host and parasite at the molecular level in parallel to the dramatic physiological and behavioural changes in the bees.

Continuation of this research on a fascinating host-parasite system will bring us closer to understanding and hopefully eventually combatting the plight of the bumble bee.

References

1. Society of Biology News Page http://www.societyofbiology.org/newsandevents/news/view/469

Author

Sive Finlay: sfinlay[at]tcd.ie

Sive is a PhD student from Trinity College Dublin, who recently won Best Biology student at the 2012 SET awards for her undergraduate project detailed here

Photo credit

Mike Kelly

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Thunder lizards + methane = climate change

Mathematics is the language of science and when it comes to biology this is no exception. It’s only when you start researching for yourself that you realise how useful a skill it is. Consider, for example, the mathematical approach that Graeme Ruxton and collaborators bring to their research in ecology and evolution. Ruxton has addressed questions ranging from the foraging radius of vultures to a hypothesis proposing that sauropod dinosaurs produced enough methane, a la modern cows, to affect the climate of the time. The latter paper does seem to ask an intractable question on first inspection given that the animals have been extinct for at least 65 million years. So how do the authors even begin to tackle their question?

Mathematically of course. To begin, they estimate the population density of sauropods during the Jurassic Period from fossil data. Then they take a medium sized sauropod like Apatosaurus louise, which weighed around 20,000kg, as a representative animal. Finally they apply a relationship which gives an indication of methane production per animal, while being careful to note the relatively shorter Mesozoic day:

Methane (litres per day) = 0.18 (body mass in kg) 0.97

Multiplying it all out and the bottom line is that these beasts could put out 520 million tonnes of methane per year into the atmosphere. Incredibly, this is comparable to modern day emissions when the effects of this are apparent to all.The upshot the authors draw is that sauropods were drivers of climate change during the Mesozoic Era. There are some uncertainties in the paper to be sure. For one, the metabolism of dinosaurs is still an unknown and this has implications for their output. But the argument seems to be a sound one and this was all achieved with some fairly basic maths.

References

1. Ruxton, GD, Houston, DC (2002). Modelling the energy budget of a colonial bird of prey, the Ruppell’s griffon vulture, and consequences for its breeding ecology. African Journal of Ecology. 40 (3) p. 260–266.

2. Wilkinson DM, Nisbet EG, Ruxton GD (2012) Could methane produced by sauropod dinosaurs have helped drive Mesozoic climate warmth? Current Biology 22: R292-R293. DOI: http://www.cell.com/current-biology/retrieve/pii/S0960982212003296

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

Todd Marshall

 

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Hot heads lead to hot flashes: the evolution of menopause

A new study has been published online in Ecology Letters by Mirkka Lahdenperä and colleagues, which suggests that competition between grandmothers and their daughters-in-law may explain the evolution of menopause. The study used a 200-year dataset of births, deaths and residency patterns in pre-industrial Finland to show that competition between unrelated females of different generations was a key component of selection for menopause.

Humans are among only four species known to lose their ability to reproduce long before they die; the others being killer whales, pilot whales and one aphid species. This phenomenon of menopause poses somewhat of an evolutionary conundrum: how could the loss of the ability to reproduce increase an individual’s fitness?

One possible answer was suggested by Cant & Johnstone, based on differences in how related a mother and daughter-in-law are to each other’s offspring. Historically, females of reproductive age usually leave their family to co-habit with their spouse’s family in most human societies, while males stay near their parents. This means that elder females are typically unrelated to next generation of reproductive females in their locale. Thus, it is expected that young females should invest in competition with their mother-in-law, while the elder mothers-in-law may be selected to cease investing in reproduction and instead invest in helping to raise their related grandchildren.

The new study by Lahdenperä et al. showed that when a mother and daughter-in-law reproduce at the same time offspring survivorship is reduced by up to 66%, while simultaneous reproduction by a mother and daughter had no effect. These patterns suggest that a daughter and mother-in-law compete strongly for resources for their children, as predicted by Cant & Johnstone.

The authors also used their data to parameterise a kin selection model to show that selection should favour menopause around the age of 50 in order to reduce this conflict. This study provides an excellent example of how theory and data can be combined to tackle evolutionary problems, and provides insight into one of the great peculiarities of the human species.

References

1. Lahdenperä M, Gillespie DOS, Lummaa V, Russell AF (2012) Severe intergenerational reproductive conflict and the evolution of menopause. Ecology Letters. (http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2012.01851.x/abstract)

2. Uematsu K, Kutsukake M, Fukatsu T, Shimada M, Shibao H (2010) Altruistic colony defense by menopausal female insects. Current Biology 20: 1182-1186. (http://www.sciencedirect.com/science/article/pii/S0960982210006391)

3. Cant MA, Johnstone RA (2008) Reproductive conflict and the separation of reproductive generations in humans. Proceedings of the National Academy of Sciences 105: 5332-5336. (http://www.pnas.org/content/105/14/5332)

4. http://en.wikipedia.org/wiki/Kin_selection

Author

Luke McNally: mcnalll[at]tcd.ie

Photo credit

Wikimedia Commons