Still Life and Science

Can you draw? Can you draw well? Chances are if you’re a biologist the answer to at least one of these questions is ‘no’. You may have studied art at school, in the same way you took French or Literature, but you figured that as a budding biologist the days of declining verbs, finding meaning in poems or sketching a vase of flowers were far behind you. Then, one day you go to an undergraduate lab session and someone says ‘look at this specimen and draw what you see”.

Draw? But I can’t draw!

I know that this is a common reaction because it was one I had myself as an undergraduate and one I’ve been seeing recently while demonstrating in labs. I found myself trying to explain that you don’t need to be able to draw to do scientific drawing but couldn’t seem to explain satisfactorily what you did need. So I thought I’d take this opportunity to say what I think is important for scientific drawings and then in comments below others more knowledgeable than myself can add their advice.

I guess the first thing to understand is the point of a scientific drawing. Scientific drawings differ from art in that they are not trying to find a ‘soul’ or convey via metaphor some deeper truth. Instead they are trying show accurately and with as much detail as possible what an organism looks like at a given magnification.

In other words, not this:

Fig 1 - Van Gogh sunflowers

but this:

Fig 2 - scientific sunflowers

The reasons for doing this are two-fold. One is for your own benefit. You may find yourself studying a multitude of specimens in detail for a period of time but if you have to stop the work for some reason then without accurate notes you will have no idea what you’ve been doing (this goes for lab notes in general, not just drawings). The other reason is to show other researchers what you are describing in text. A picture is worth a thousand words, so the saying goes, and given the technicality of the language of many fields of science, it also makes understanding easier. You may think that photography has superseded the need for line drawings but surprisingly not. Photos that capture all the details required can often be extremely hard to take: getting the exposure, angle and perspective correct can be very difficult, especially for small or otherwise fiddly objects.

I realise that the scientific drawing above is beyond the skills of most of us, but there are ways to achieve a certain level of technical ability without possessing any artistic merit. If I may indulge in a personal anecdote, I cannot draw. I gave up art at school as soon as I was allowed and in that time I never progressed beyond drawing three-dimensional boxes (though I was really good at them!). Yet I have done a scientific drawing that was suitable for publication1:

Fig 3 - anglerfish

The point is not to gloat (honestly, who would gloat over that!) but to say that if I can do it, anyone can!

So, how do you do it? There are a few pieces of equipment that are essential in my view. These are:

  • Sharp pencil (a ‘clicky’ pencil with a hard (HB) lead is ideal)
  • Plain paper
  • Ruler
  • Eraser

The ruler may seem strange at first but if you are making any attempt at accuracy proportions are key. I’d even go so far as to say if you have one to hand, use a protractor to help with angles as well.  The main problem I’ve seen is students getting the proportions wrong because they are drawing solely by eye. Measure the size of parts and translate that to the page. If you can do a one-to-one scale then great but if that’s not possible then factor up or down as necessary. Make notes if you have to. To draw the illustration above I had a page covered in all the various measurements, from the length of the appendages (it’s the lure of an anglerfish, if you’re wondering) right down to the size of the larger spots. The purpose wasn’t to make a beautiful illustration (which is good as it isn’t) but to show other researchers as clearly as possible the key feature used in identifying the fish.

It’s really helpful if you can poke around the specimen you are trying to draw, if possible. Something may look completely incomprehensible but if you lift it or tilt it, it can often suddenly make sense. It’s really hard to draw what you don’t understand. Label parts if you can, especially if you’re making a first draft. The more information the better. You never know what detail may become important and if you haven’t noted it then you may regret it (I had to go half-way round the world to re-examine that fish because I didn’t make good enough notes and drawings the first time).

It will take several attempts to do a really good illustration and obviously in labs you don’t have that sort of time but you can still use them to start developing your skills. You can also practice. It’s really easy: just find a biological object (shells are really good) and try and draw it as accurately as possible. You will get through lots of paper, rub out lots of lines and probably swear and get frustrated, but you can draw scientifically. And, which is ultimately the real reason for doing scientific drawings, the close study required to achieve this will help you understand the specimen in deeper and more complete way.

Good luck and enjoy!

1. Hearne S. (2009) First record of the anglerfish, Himantolophus appelii, from the Falkland region. JMBA2 – Biodiversity Records. 2: e152

Author:

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

Image Sources: Wikicommons and Sarah Hearne

 

Blog-tastic!

Seminar

Andrew Jackson and I started a new module this year called “Research Comprehension”. The aim of the module is simple: to help students to develop the ability to understand and interpret research from a broad range of scientific areas, and then to develop opinions about this research and how it fits into the “big picture”. In our opinion, this is perhaps the most important thing an undergraduate can get out of their degree, because no matter what you do when you graduate, in most jobs you will be expected to read, understand and interpret data. Often this will be in a subject you are unfamiliar with, or use unfamiliar methods or study organisms. So being able to understand this information is key!

The module revolves around the Evolutionary Biology and Ecology seminar series in the School of Natural Sciences, so the topics are broad and cover whole organism biology, molecular biology, genetics, plants, and animals etc. Students attend the seminar on a Friday and read some papers sent on by the speaker. There is then a tutorial on a Monday with a member of staff who has interests in the area of the seminar. This gives everyone a chance to clear up any confusion and to discuss what they liked (and disliked) about the seminar. The continuous assessment for the module is in the form of the blog posts we will post here. Thus the module also aims to improve the students’ abilities to communicate all kinds of scientific research to a general audience, a skill that is currently in great demand.

From next Wednesday onwards we will select a few blog posts to put onto EcoEvo@TCD. These may not necessarily be the posts that get the best grades, but they’ve been chosen to reflect the diversity of angles the students have taken to communicate the parts of the seminar they found most interested. Overall we’ve been extremely impressed with the quality of their blog posts, so we hope you enjoy reading them!

Author: Natalie Cooper, ncooper[at]tcd.ie, @nhcooper123

Image Source: Jorge Cham, www.phdcomics.com

Kenya- A Summary through the vegetation

Campsite at Ol Pejeta, with Acacia xanthophloea in the background.
Campsite at Ol Pejeta, with Acacia xanthophloea in the background.

During the first week of November I travelled to Kenya to help out on the Tropical Field Ecology course, run by Ian Donahue in the Zoology Department.  Final year students from Zoology, Environmental Sciences, and Plant Sciences attended, and I was the postgraduate representative from the Botany Department.  While I should under no circumstances be considered a true Botanist-I study plant-animal interactions, and my botanical skills are mediocre at best- I did my best to learn about the amazing tropical flora of this region.  I’m sure others will write about the trip in detail, but I thought I would summarize our experience using the dominant or interesting plants we saw in each place we travelled.

Day 1&2- Arrive in Nairobi: After spending the night in the United Kenya Club, we awoke to a 5 hour drive north to Laikipia County.  Along the way the most striking plants were ornamental and known to a number of the students already- for example, colourful Bougainvillea was visible from quite a distance, as were the beautiful flowering Jacaranda trees- neither of course are native to the region.

Day 3-Ol Pejeta Conservancy, Laikipia County: We camped for the next two days in Ol Pejeta, and although we experienced quite a bit of rain, it was one of the most beautiful places I’ve ever seen.  The campsite was on the river and surrounded by Acacia xanthophloea, known to the locals as “Yellow fever acacia” for its medicinal properties.  It has a yellow-green bark which makes it quite distinctive.  On game drives we saw a lot of scrubby shrub species, none in flower.  It was difficult to identify many of the species in the conservancy but we were told many of them belong to the genus Euclea.  We also got our first glimpse of Solanum incanum but more on that later.

Solanum incanum at the Chimpanzee sanctuary in Ol Pejeta
Solanum incanum at the Chimpanzee sanctuary in Ol Pejeta

Day 4- Nakuru: Compared to Ol Pejeta the flowering flora here was a breeze to identify! Although a lot of it comprised invasive species, such as Lantana and Datura species, and of course the conspicuous Solanum incanum (also known as Sodom’s Apple).  S. incanum gives the management at Nakuru serious trouble, growing uncontrolled in areas that are over grazed or disturbed by humans.  In addition to the invasives we saw a lot of Leonotis mollissima and identified a lovely shrub called Tarchonanthus camphorates from its camphor scented leaves.

Day 5-11-Baringo County: And finally, after quite a lot of driving (during which we saw some impressive Euphorbia candelabra specimen), we arrived in Baringo County.  Our first day here we went for a hike at Lake Bogoria, and spotted two species of interest.  First, the indigenous Adenium obesum, or Desert Rose.  Some of the students carried out their mini-project on the nectar secretion and flower visitation of this species, and found nectar volume varies with time of day.  Second, we saw Salvadora persica, known as the “toothbrush tree.”  Our local guide told us people chew the twigs to promote dental hygiene.  Throughout the county, two new species of Acacia were also evident- Acacia tortilis (The Umbrella Thorn, accurately named after its shape) and Acacia mellifera.  Women in the area highly value A. mellifera because the honeybees they keep apparently favour it for making particularly sweet honey.  And finally, one cannot forget to mention the damaging invasive Prosopis juliflora.  Native to Mexico and Central America, it was introduced to try and control soil erosion and now has spread throughout the county.  It is difficult to remove as it can regenerate from the roots, and is not particularly useful as fuel, food for livestock or fencing.

Adenium obesum, Desert Rose at our campsite in Baringo, Robert’s Camp
Adenium obesum, Desert Rose at our campsite in Baringo, Robert’s Camp

This description is simply the most obvious vegetation we saw on the field course.  The diversity of flora and fauna was overwhelming and I think the students, demonstrators, and staff alike were impressed and awed by the environments we were fortunate enough to experience.  Kenya is truly an amazing place!

Author and Picture Credits;

Erin Jo Tiedeken, tiedekee[at]tcd.ie, @EJTiedeken

SQUIRREL PLAGUE! Or “Don’t hug a dead squirrel”

Squirrel

During my PhD I worked on the morphological evolution of New World monkeys, phyllostomid bats, Australasian possums, and ground squirrels. For some reason the only part anyone outside academia (and some people in academia) remembers is that I like squirrels. This means that whenever there is a squirrel-related news story, around half a dozen people send me a link and/or want my opinion.

So this July I got sent a lot of copies of this story: “Squirrel infected with the BUBONIC PLAGUE closes major US campgrounds” (the Daily Mail clearly decided the words bubonic plague weren’t shocking enough so they put it in capital letters; sophisticated journalism at its best).  This was less shocking to me than most people expected, because I have an interest in zoonotic diseases (diseases transmitted from animals to humans) and was already aware of the continued existence of plague. However, in light of the over excitement in the media, I thought I’d write a quick blog post about plague and try to clear up some of the confusion.

When most people think of bubonic plague they think of the Black Death in the 14th Century. This is definitely the most famous and most devastating outbreak of plague – it wiped out 30% of the population of Europe and contributed to major changes in society and agricultural practices across the continent. Other famous outbreaks include the Great Plague of London in the mid 1600s which only ended after the Great Fire of London in 1666. Improvements in sanitation have all but eliminated dramatic outbreaks of plague in the developed world, but it is still is a significant problem in Africa (particularly in Madagascar and the Democratic Republic of Congo), Asia and South America, which report around 2000 cases every year with a global fatality rate of 5% to 15%.

There are three major forms of plague: bubonic, septicaemic, and pneumonic. They are all caused by the bacterium Yersinia pestis but have different symptoms, fatality rates and transmission modes. Bubonic plague is the “traditional” Black Death version of the plague with the black necrotic swellings which lead to blood infections, bleeding, shock, organ failure and eventually death. Septicaemic plague has all the same symptoms but without the initial swellings. In both bubonic and septicaemic plague the bacteria are passed from host to host via flea bites, and both are fatal around 50% of the time if no antibiotic treatment is given. Pneumonic plague on the other hand, has an almost 100% fatality rate if untreated, is transmitted by inhalation of airborne droplets, and mainly affects the respiratory system. So really nasty stuff! Luckily most strains of Yersinia pestis respond well to antibiotics.

Although it’s not a major problem because outbreaks are rare and plague can be treated with antibiotics, the disease is still endemic to the southwestern states of the USA. This means the disease is naturally found there. The natural reservoir population for the disease consists of ground squirrels and other small rodents. Often outbreaks occur in humans after a major outbreak in the squirrels results in humans handling dead or dying squirrels. A few years ago a case in a little girl in the USA was due to her finding a dead squirrel and giving it a decent funeral! So unless you go around playing with dead squirrels, there is very little chance of you catching the plague. Before you panic about that dead squirrel you picked up last week, note that when I say “squirrel” I’m referring to a group of rodents (technically called the Sciuridae) that contains just under 300 species (depending on how you count them!), two of which are the red (Sciurus vulgaris) and grey (Sciurus carolinensis) squirrels we have here in Ireland. Mostly the squirrels infected by plague are ground squirrels, not the tree squirrels we’re all most familiar with. Ground squirrels, unsurprisingly, live on the ground and in burrow systems and include things like marmots, prairie dogs and chipmunks. This means that unless you’re handling some dead exotic migrant squirrel, in Europe at least, you’re probably fine! In summary, all fine, totally natural, totally treatable by antibiotics, nothing to see here, DON’T PANIC!

This post was meant to be all about making everyone feel better but then I ended up reading the World Health Organisation (WHO) website. After all this positivity, here’s the scary bit! Naturally multiple-drug-resistant strains of the bacteria have been identified in Madagascar, and antibiotic resistance appears to be easily transferred between bacteria via plasmids in the flea mid-gut. So unfortunately the age of easily treating plague with antibiotics may soon be over. I was also a bit puzzled by the WHO website because although there are quite a lot of diseases out there, WHO has vaccine development programmes for only a few. One of these diseases is the plague. It turns out that bubonic plague is a big worry because it could be used as an agent of biological warfare. In fact, historians suggest that plague was one of the first biological weapons; soldiers would throw plague-infected corpses over castle walls during sieges in the 14th century.  More recently, the Japanese forces near the end of World War II had devised “Operation Cherry Blossoms at Night” to send kamikaze bombers with the plague to infect San Diego, but were stopped by the atomic bomb being dropped on Hiroshima just a month before the planned attacks. The USA and USSR also experimented with aerosolized plague in the 1950s and 1960s, before the Biological Weapons Convention (BWC) was passed in 1972 forbidding offensive research into biological weapons. However, not all countries or organisations believe in the goals of the BWC or the Geneva Convention, and aerosolized, antibiotic resistant, pneumonic plague, which as I mentioned above is almost 100% fatal if untreated, remains one of the most frightening and deadly, potential biological weapons around, particularly given the high mortality rate and ease of rapid person-to-person transmission. Something to think about next time you try and hug a dead squirrel…

Author:

Natalie Cooper: ncooper[at]tcd.ie

@nhcooper123

Photo source:

Wikicommons

Cape Vulture Conservation

Cape-vulture

Conservationists try their best to stop endangered species sliding to extinction and keep the habitats of these life forms intact. Captive breeding programs, national parks, management of invasives etc. are all common measures in conservancy. But how do we know that these methods work? Perhaps an invasive species is actually serving as a food source for the conservation target, and, by killing off the former, we imperil the latter further still. Fortunately, we can avoid such disasters through experimentation and modeling, in other words, with some good science.

Consider the case of the Cape Vulture (Gyps coprotheres) in Southern Africa. This large scavenger patrols its habitat, often a huge range, foraging for carrion. It’s suffering a decline in numbers for a variety of reasons. Carcasses are often poisoned to kill predators that take farmer’s livestock with the vulture an innocent victim. Their social nature means tens of the birds can be killed by a single toxic carcass. More direct persecution comes in the form of poachers who have taken to poisoning the carcasses of their quarry. The rationale is to wipe out vultures who will identify the location of future crimes. Then there are accidental deaths that arise from bird collisions with electricity pylons and wind turbines. And it will take some time to convince otherwise those who value vulture brains for their clairvoyant properties.

Fortunately, some vultures survive these incidents and that’s where rehabilitation centres come in. People at these facilities nurse the birds back to health and release them into the wild. The problem is some of the injuries suffered may be insidious, leaving a permanent but unnoticeable effect on the animal’s health.

We used resightings data on a population comprised of rehabilitated and wild birds to estimate their chances of survival and found that the rehabs have a significantly lower chance of surviving year on year (90% Vs 72%). By modeling different proportions of rehab and wild birds we showed that a 50:50 mix of the two groups is the threshold beyond which the population will decline.

That’s not to say that we think rehabilitation is a bad idea, it’s obviously better to get the bird back in the wild where it can contribute to the survival of the species than leave it to die from its injuries. Rather we suggest that vulture conservation should be focused on prevention instead. This is achievable. In India, farmers have stopped using drugs on their cattle which poisoned the vulture population en masse. Pylons and turbines can be equipped with signals that alert the birds to their presence.

Conservation practice coupled with a scientific understanding can only better our ability to stop the slide to extinction.

Author: 

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

Photo credit;

Phil Perry

How Good is the Fossil Record?

crinoid

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Author and Picture Credit:

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

Conference season madness!

ConferenceLogos

Over the last month or so you’ll probably have noticed that a lot of posts on EcoEvo@TCD are essentially “what I did on my summer holidays” essays. Luckily, I think most of us did quite a lot of interesting and scientifically relevant things! My summer this year seemed to be full of conferences, so I thought I’d write a quick post describing them, and what I liked or disliked. This post was inspired by Britt Koskella’s excellent post on the same subject; although Britt attended NINE conferences this summer so is clearly completely insane.

Over the summer I attended four international conferences: Evolution 2013 in Utah, BES Macroecology in Sheffield, International Mammalogical Congress in Belfast, and ESEB 2013 in Lisbon. This involved 15 days of conference going, four plenaries, one prize talk, eight invited talks, 103 standard talks, and 56 lightning talks. So in total I spent about 40 hours in talks, not including questions or people running over time…

Evolution 2013, attended by around 1500 people, was in late June, and was probably my favourite conference academically. I’ve been going to Evolution since 2006 and have only missed three meetings in that time, so it’s the conference I know the most people at, and is most closely aligned with my interests in macroevolution. Most of the top names in the field were there, and I saw some excellent talks. I particularly enjoyed the plenaries. Richard Lenski’s plenary reviewed 25 years of experimental evolution using E.coli in his lab, Dolph Schluter’s discussed ecological opportunity as a factor in increasing rates of diversification, and Jack Sullivan talked about advances in systematics since the last meeting at Snowbird (although this talk was mainly notable for the “dirty chipmunk sex” and pictures of ground squirrel bacula – look them up on Google!). The plenaries at Evolution are generally entertaining and thought provoking, and in recent years there seems to be a trend to talk about something controversial. This is great and I think that’s how plenaries should be! The other big highlight was the location. It was up in the ski resort of Snowbird at 8,000 feet, so we were surrounded by snowy mountains, cheeky ground squirrels, marmots and even the occasional moose. On the flip side, this year’s Evolution was smaller than usual (or felt smaller) because fewer European scientists made the trip. With ESEB (the European equivalent of Evolution) and INTECOL happening in August many people decided to attend these instead. This made it feel a bit more US-centric than usual.

My second conference of the summer happened two days after I got back from Utah and was in the less exciting location of Sheffield (sorry Sheffield, you just don’t have enough moose). This was a much smaller conference with only 60 attendees. The great thing about this was that I was able to briefly chat to almost everyone at the conference. In addition, many of the attendees are old friends of mine so it was lovely to catch up with them. This was a British Ecological Society special interest group meeting on Macroecology (if you’re UK or Ireland based I’d definitely recommend checking out any of the BES special interest groups, they’re friendly and full of enthusiastic people!). We spent the two day meeting listening to five minute talks from anyone who wanted to present, then had panel discussions after the talks which worked really well. We also had some “break out” groups to discuss the future of the field. The most interesting of these for me was – “If we got £20 million from the government today what would we spend it on?” Amusingly this mostly boiled down to people wanting more, and better quality, data! The highlight of this meeting for most people was Ethan White’s excellent plenary. I’m sure it would have been mine too but I had issues with my train and ended up being two hours late and missing his talk (sorry Ethan!). The train also “ate my homework” (I had to stand all the way on the later train so didn’t get chance to write my talk). I promise to do better next year!

My third conference was the 11th International Mammalogical Congress in Belfast. Full disclosure – I’m not really a mammalogist (I work on mammals, but just because the data is good) so this was an odd one for me. But Belfast is only two hours away on the train and my PhD students thought it would be fun to present their posters more than once. Organisationally this was a strange conference (no offence intended). The talk program wasn’t online so there was a lot of frantic flipping through the booklet to try and find talks. There had also been a change to the program that removed the second poster session, meaning that one of my students turned up a day late to present his poster. However, I saw some really interesting talks, particularly in the disease ecology symposium. I also saw the worst set of PowerPoint slides I’ve seen in a long time – lemon yellow background, brown text with shadows, no pictures and text completely covering each slide! Yeurgh!

My final conference of the summer was ESEB 2013. This was a lot of fun and I saw some excellent talks. I also discovered that I don’t understand population genetics. At all. I think by this point I was “conferenced-out” so it was a difficult conference for me. Also because of the overlap between INTECOL and ESEB, a lot of people I would normally catch up with there were at INTECOL instead. This was particularly reflected by the paucity of macroevolution talks and attendees with macroevolutionary interests. In fact, our delegation (myself and five students) from TCD was probably the biggest group of macro-people there! This meant there were a few days where I found it hard to find many relevant talks. I still attended some very interesting talks, but I also spent a lot of time feeling very stupid because I attended lots of talks I didn’t understand at all! The highlight of this conference for me (partly due to my macroevolutionary interests, partly due to my love of pretty slides) was Rich FitzJohn’s JMS prize talk. The content was good but the slides (all made in R apparently!) were gorgeous. I also really enjoyed Hannah Kokko’s talk where she was able to describe quite complex maths in a really accessible way. The other, less academic, highlight was tweeting a picture of some Superbock – a local beer – and the beer company replying, thus ruining the conference twitter feed by filling it with pictures of beer! Oops!

My conclusions:

1)Four conferences in a summer was too many conferences! Each was fun in it’s own way, but conferences are exhausting both mentally and physically (often talks start early and social events end late) so I ended up feeling totally wiped out for weeks afterwards. Next year I think I’ll focus on two or three at most.

2)Feeling stupid at a conference is inevitable at some point, but it doesn’t mean that you are stupid. When I was a PhD student I felt stupid all the time, but as I’ve become more seasoned I’ve realized that often it’s because the speaker isn’t explaining themselves properly, or because it’s so far out of my field that I don’t know the background. If you don’t understand, try and discuss it with others afterwards. We’ve been doing this a lot after seminars recently and it’s really helped my understanding of the trickier bits.

3)Big conferences are great for meeting lots of people you know already, but terrible for making new connections. From now on I’ll try and go to one big conference a year to catch up with old friends, and one small conference where I can meet new people.

4)Going to four conferences made me realize how cliquey a lot of evolutionary biology is. Many of the people speaking in symposia had also spoken at symposia in previous years. In some cases people spoke in symposia at multiple conferences (and gave almost the same talks). This is inevitable to some extent and shows the importance of having a good network within your subject. Next year however, instead of moaning I’m going to organize my own symposium and try to invite some people I don’t know, plus women and early career researchers. I’m also going to make more of an effort to attend small conferences where I don’t know lots of people.

5)Twitter is an awesome way to improve your conference experience (see my other blog posts on this). But don’t tweet too many pictures of Superbock…

Author: Natalie Cooper, ncooper[at]tcd.ie, @nhcooper123

Trophy Hunters

Antler collection at Harvard's Museum of Comparative Zoology
Antler collection at Harvard’s Museum of Comparative Zoology

It may be an inconvenient truth in these conservation-focused times but we owe a debt of gratitude to the trophy hunters; the army officers and colonial-types who killed animals for sport and prestige. Without their considerable efforts, the vaults of natural history museums would be devoid of the skeletons and skins which form the bases of both exhibitions and many PhD and MSc. theses. Of course, were it not for the over-zealous efforts of hunters perhaps many charismatic animal species wouldn’t be so endangered now but let’s focus on the positives here…

Naturally, if you’re a hunter looking for a prize, bigger is usually better. It’s far more impressive to have a stag or bear’s head mounted on your wall than a hedgehog or shrew – although I would like to hear the embellished stories which might arise from tales of killing your first hedgehog! Similarly, if you are a taxidermist or museum collections manager in many ways it is easier to prepare and preserve large rather than small mammal specimens.

These collection trends are all well and good if you’re interested in the charismatic species. I, however, am studying the little shrewy-type things; hedgehogs, moles, shrews, golden moles and tenrecs – fascinating species but not prized possessions for your trophy case. Even in some of the world’s largest natural history museums it’s difficult to find intact skulls and skeletons of some of these creatures. Combined with the inherent delicate nature of these animals (some tenrecs’ limbs are tiny!) compiling a complete morphometric data set of the groups remains challenging.

Tenrec limbs with a pen for scale; teeny tiny tenrecs!
Tenrec limbs with a pen for scale; teeny tiny tenrecs!

For the museum collections of these little critters that do exist; I am eternally grateful to the progenitors of carefully handwritten labels accompanying the skulls and skeletons on which my PhD research depends. Adventurers such as Major Forsyth, G.K., Creighton, and C.J., Raxworthy who donated specimens from their tropical voyages deserve special thanks in any research which arises from their collective efforts. However, I am also grateful to the back-yard naturalists, the people who collected and preserved the seemingly ordinary, every-day species of common shrews and hedgehogs which are no less important to ecological and evolutionary research than their exotic counterparts. I benefitted greatly from their collective efforts during my recent trip to Chicago’s Field Museum.

Whether naturalists or trophy hunters, the individuals immortalised by museum specimen labels couldn’t possibly have envisaged all of the diverse future research which would be based on their prized collections. It’s an important reminder that, despite the inherent appeal of flagship species, the lesser-spotted or common-something-or-others are just as deserving of our attention and study. Even if you don’t have the equipment or inclination to start posting skeletal remains of common species to your local natural history museum, there are still plenty of ways of contributing to the study of “ordinary” wildlife. Don’t be dazzled by the allure of large-animal trophy hunting and remember that, when it comes to understanding the natural world, bigger is not always better.

Author:

Sive Finlay: sfinlay[at]tcd.ie

@SiveFinlay

Photo Credits

Sive Finlay

How do Lego cars evolve?

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The ESEB conference this August in Lisbon was not only about Drosophila and #superbock. Among the useful discussions and the interesting talks, a definite highlight came from our very own Kilkenny scaling man all about time perception and comparative analysis… Argh no I missed that one – apparently there was even a realistic Tiger Beetle hunting impression! There were at least eight overlapping talks at any one time and, as I had already seen Kevin’s talk, I went to listen to Folmer Bokma’s insightful talk instead.

I felt Bokma’s talk was a good follow-up to Gene Hunt’s excellent talk on gradualism vs. stasis which he demonstrated through his careful study of the Ostracod fossil record, recently published in the excellent August issue of Methods in Ecology and Evolution. By means of a lengthy introduction with citation of more or less unknown people such as H. Falconer and C. Darwin, Bokma emphasised the fact that examples of evolutionary stasis are well known from the fossil record and that ideas of species undergoing rapid adaptations that were not specifically linked to environmental changes have been around since the 19th century.

Bokma argued that trait co-adaptation is an important source of evolutionary changes. He cleverly illustrated this argument by means of a Lego car; I always think that using something other than just slides in a presentation greatly improves the talk! He argued that changes in colour or shape attributes can happen “easily” over a short evolutionary period as an adaptation to environmental changes. For example, characteristics of fur in Vulpes vulpes/lagopus foxes (the colour of the Lego car) or beak sizes in Darwin’s finches (the windscreen of the Lego car) have evolved to increase the fitness of the individuals living in particular environmental conditions.

But things get trickier when it comes to major changes or adaptations. Bokma illustrated this idea by trying to change the overall shape of the car (like going from a regular car to a truck). As soon as he started to remove one wheel, the car totally lost its fitness! For non-Lego fans he also gave the example of enzymatic reactions in endotherms: if just one enzyme evolves to be more active at a temperature different to normal body temperature, then there is no increase in fitness for the organism (and probably a decrease as that precise enzyme will be less efficient). It is only when all enzymes co-evolve to be more active at a different body temperature that there might be an increase of fitness for an individual. Bokma used this example to emphasise the irreversibility of evolution and how lineages can get stuck in “evolutionary dead-ends”. In response to H. Falconer’s comment to Darwin (1862) that the Elephant remains “unchangeable & unchanged”, Bokma argued that it might be “easy” (in an evolutionary way) to become an elephant but once you’re there, climbing into trees or crawling underground becomes tricky. So for these bigger evolutionary changes (the “jumps” in punctuated equilibrium theory), one needs a “genetic revolution”; evolving from a flightless theropod to a turkey involves co-adaptation of more than just locomotory characters. There is a strong irreversibility component to evolution.

While some people were kind of miffed by Bokma’s talk and started a polite but energetic debate involving genetic mumbo jumbo, I just thought that his talk was a great illustration of the problem of stasis and jumps in evolution. As Gene Hunt demonstrated, evolutionary stasis and jumps are clearly dominant in the history of life but they are trickier to explain than gradualist evolution. However, to be objective I have to agree with some of the general comments on Bokma’s talk; “So what? We already knew that.” It reminded me of S.J. Gould’s excellent review on part of this idea in the Panda’s Thumb (1980): The Return of the Hopeful Monster. So yes, we do already know about the ideas Bokma presented and he didn’t bring any staggering new insights but I believe he illustrated it with talent and brio! And perhaps I should mention that I can’t be completely objective here; I just love Lego, sorry.

Author

Thomas Guillerme: guillert[at]tcd.ie

@TGuillerme

Photo credit

creator.lego.com

Sea Serpents off the Port Bow!

Below the thunders of the upper deep,

Far far beneath in the abysmal sea . . .

[Tennyson, The Kraken]

Strange things are stirring from the deep. Creatures from myths and legends, the sea serpents of old, are descending upon our shores to warn us of impending doom. . .

Well, maybe not. But the news that not one but two mysterious oarfish have been found dead and beached in California recently has spread around the world, reminding people that the oceans still harbour creatures that are stranger and more alien to us than even the most hallucinogen-induced science fiction creations.

Oarfish are members of the genus Regalecus. There are three species, R. glesne, R. kinoi, and R. russelii, found in the Atlantic, Eastern-Central Pacific and Indo-Pacific respectively. They are the largest bony fish in the world and can reach over 11m in length. Very little is known about them. Unfortunately most of the published literature concerns their meristics which are important but make for incredibly dull reading.

Oarfish picture
Oarfish

Regalecus is one of two genera in the family family Regalecidae. The other genus, Agrostichyhtys, is monospecific and contains the species A. parkeri, commonly known as the ribbonfish or streamerfish. A. parkeri is even less well-known than the oarfish. Wikipedia says that it is known from only seven specimens, though I know this is an underestimate as I have personally seen and dissected two that are not included in that list and I’m sure there are more in museum and fisheries department basements around the world that just haven’t made it into the literature.

Agrostichthys parkeri
Agrostichthys parkeri

There are a number of reasons the Regalecids are so poorly known. They live in the open ocean and if caught at all it is usually as part of a commercial catch where scientific research is low down the list of priorities. Their delicate shape also means that they damage easily and often what is hauled on board is barely recognisable as fish, let along as a Regalecid.

Another reason is that they elude scientific surveys as they are perfectly camouflaged and are almost impossible to see. I know this may sound crazy – an 11m long shiny silver animal with a gigantic eye surely can’t be hiding, it’d be like dressing up as a mirror-ball and expect to be able to blend into the background. But actually, that’s precisely what they are doing.

Their morphology has evolved for a very specific environment: the mesopelagic zone. This zone, colloquially termed the ‘twilight zone’, is the transitional part of the ocean, where light is still visible when you look up but there is nothing but blackness when you look below. A fish that is swimming in the water column will be seen as a black silhouette against the light when viewed from below or will stand out against the black of the deep when viewed from above.

Mesopelagic zoneThis makes mesopelagic fish vulnerable to predation so they have evolved a number of countermeasures. The first is to be laterally compressed. This means that there is less of them to block or reflect any light. If you cannot compress laterally then a second option is to countershade – make your belly light and your black dark. Pelagic sharks, fish and even birds do this – it’s why penguins wear tuxedos.

Now that attacks from above and below have been dealt with, attacks from the side must next be tackled. For this, light contrast isn’t so much of a problem, but uniformity is as fish present a uniform block of colour against a dappled background. And this is where the silver comes in. The reflective surface of the fish, combined with their undulating body, help break up the light and allow it to merge into the background. If you don’t believe me watch this video of an oarfish in its natural habitat.

These adaptations mean they are able to successfully hide from all but the luckiest of predators. Yet life is more than just about avoiding being eaten. It’s also about finding food. This is incredibly difficult in the sparsely populated open oceans. and it is here that the giant eyes come in. Unlike the bathypelagic zone where eyesight is largely redundant, here in the mesopelagic zone there is just enough light to see by. You’ll notice the large pupil which has evolved to catch every last photon of light in order to detect potential prey, who, it’s worth pointing out, have evolved the same anti-predation adaptations as the Regalecids. If you watch the video you’ll see that oarfish sit vertically in the water column, looking up towards the ocean surface so they can fully exploit their excellent vision and spot anything passing overhead. Prey are few and far between, and are constantly on guard against being eaten. To catch anything stealth and speed are essential. And this is where their weirdest adaptation comes into play.

Before I continue, I want to point out that what follows is pure speculation as I can find nothing in the literature that discusses this, the most bizarre aspect of Regalecid morphology. I thought it was unique to A. parkeri but closer inspection of photos and videos (this is R. russelii) indicates this is a feature common to the family. I am talking about their mouth.

At rest there is little of note.

retracted

It’s a bit strange in appearance, almost beak-like, but fish have evolved all sorts of weird appearances. Nothing to worry about, maybe.

Think again.

extended

The ‘beak’ extends! It forms a sort of funnel and we (my former colleagues and I) speculated that this might be to try and change the water pressure to help suck prey in. The narrow tube quickly opens up into the wider ‘pouch’ towards the back. This suggests there will be rapid changes in water pressure but without proper study, and live observations, this is all complete conjecture which is crying out for research.

As if all that isn’t enough to pique your interest, there are reports that the live fish give electric shocks:

Jason McKenzie reported that when he picked up the fish . . . he experienced what he described as mild but quite distinct pulsed electric shocks that passed up through his hand into the forearm at intervals of about 10 s. A companion who independently held the fish reported the same sensation.1

There is nothing coherent I can say about that; it just blows my mind!

It’s a real shame the media frenzy has been so superficial. There is so little known about these animals: basic biology such as how long they live, how often they reproduce, how they find mates, what they eat and what eats them is all unknown. These new specimens will undoubtedly be studied exhaustively. The media hype will have died down by the time the results are published, but I recommend keeping an eye out as they will add so much more to the understanding of these magnificent, elusive animals.

1 McDowall, R M & Stewart, A L (1999). Further specimens of Agrostichthys Parkeri (Teleostei: Regalecidae), with natural history notes. Proceedings of the 5th Indo-Pacific Fish Conference, Noumea, 1997. pp165-174. Séret, B & Sire, J-Y, eds. Sociéte Française d’Ichthyologie, 1999, Paris. 

Author and Picture Credits: Sarah Hearne, hearnes[at]tcd.ie, @SarahVHearne