Before training your dragon, print a 3D tail for him

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3D printing (or additive manufacturing, AM) describes any of the various processes used to make a three-dimensional object. In 3D printing, additive processes are used, in which successive layers of material are laid down under computer control. While its limitless potential in manufacturing, the construction industry, transportation and human health has been widely recognized, 3D printing also plays a significant role in animal protection and conservation.

Several cases of using 3D printing for animal assistance have been reported during the past few years. Although artificial limbs have been used to help poor dogs and other animals who lost their legs, 3D printing makes the design and manufacture of the limbs far easier. And, thanks to the well developed 3D-scanning technology, the printed limbs are more efficient and comfortable for animals. Just see how happy this dog is.

Birds also benefit from 3D printing. This bald eagle and Costa Rican toucan both received printed beaks which will hopefully improve their chances of survival. And a tortoise has even been given a new shell thanks to 3D printing technology.

3D printing can be also applied to animal conservation in the wild. For example, the Wildlife Conservation UAV Challenge uses 3D printed drones to save endangered animals from poachers. 3D printing has also been used to build animal habitats including hives for bees, artificial reefs for fish, and nests for birds.

For the sake of scientific education, 3D printed models of skulls, organs and muscles can be used for demonstrations and detailed observations. In research, the technology can play an important role in studies of animal behavior and physical ecology. For example, 3D printed birds and fish can be used to explore how animals adapt to hydraulic resistance.

The wide-ranging potential for using 3D printing in animal protection and conservation seems limitless!

Author: Qiang Yang (Marvin), @MarvinQiangYang

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Looks can be deceiving

Small Madagascar Hedgehog Tenrec

We are all taught not to judge a book by its cover, it’s what inside that counts. Our new paper published in PeerJ shows that the same is true for tenrecs.

These cute Madagascar natives are often used as an example of a mammal family with high morphological diversity. It’s easy to see why: there are tenrecs which resemble shrews, moles, hedgehogs and even otters. These differences are even more remarkable when you consider that tenrecs are more closely related to elephants and aardvarks than they are to any of the small, “insectivore” mammals. One of only four native mammal clades in Madagascar, it appears that tenrecs have undergone an adaptive radiation to fill otherwise vacant, small mammal niches, evolving convergent similarities to other groups in the process.

Tenrecs are clearly very diverse in their appearance. However, prior to our study, no one had tested whether this apparently high diversity was more than skin deep. We tested whether tenrecs were more morphologically diverse than their closest relatives, the golden moles.

We measured the morphology of tenrec skulls and compared their diversity to the shape of golden mole skulls. This meant spending hours poking around the collections of natural history museums and many more hours placing landmarks on skull pictures for 2D geometric morphometrics analyses (Spotify was my friend!)

Pictures of an otter shrew tenrec (Potamogale velox) skull showing that landmarks (points) and semilandmarks (curves) that we used to summarise skull shape. See the paper for more information.
Pictures of an otter shrew tenrec (Potamogale velox) skull showing that landmarks (points) and semilandmarks (curves) that we used to summarise skull shape. See the paper for more information.

Tenrecs occupy a wider range of ecological niches (fossorial, arboreal, terrestrial and aquatic) than golden moles so we expected that tenrecs would be more morphologically diverse than their cousins. However, we found that tenrec skulls only have more diverse shapes than golden moles when we compared them in lateral (sideways) view but not dorsal or ventral views. These results show the importance of measuring morphology in many different views to gain a more complete understanding of overall morphological diversity.

The tenrec family includes species which convergently resemble many other, un-related small mammals. However, most tenrecs (19 out of the 31 tenrec species in our analysis) belong to the shrew-like Microgale tenrec genus. So, although many people tend to focus on the strange and unusual species (such as the otter shrew, hedgehog tenrec or the bizarre lowland streaked tenrec), most tenrecs are small, shrewy-type creatures that look very similar.

Microgale cowani
Microgale cowani

We tested whether the similarities among the Microgale tenrecs might be masking higher morphological diversity in the rest of the family. We repeated our analyses to compare the diversity of golden mole skulls to a sub-set of the tenrec family (including just 5 of the 19 Microgale species).  In this case, tenrec skulls were more morphologically diverse than golden mole skulls in all comparisons (skulls in dorsal, ventral and lateral view).

Overall, our results indicate that, while there are clear physical differences among tenrec family members, the majority of tenrecs are quite morphologically similar to each other so morphological diversity in the family as a whole is not as big as it first appears. Of course comparing skull diversity is just one aspect of overall morphology – analysing the shape of other traits such as limbs could yield different results – but our study represents the first step towards a greater understanding of the ecological and evolutionary diversity of tenrecs.

It’s also testimony to the fact that you should never judge a tenrec by its cover.

Author: Sive Finlay, @SiveFinlay

Everything’s Better Down Where It’s Wetter: Benthic Ecology Meeting 2015

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Conference attendance can really impact your development as a Ph.D. student and give you great ideas for future collaboration and research. In March, I was lucky enough to attend the 2015 Benthic Ecology Meeting (or Benthics) in Quebec City, Canada.  The Benthics meeting focuses on the ecology of the bottom layer of water systems, and this conference is mainly marine in focus. There were lots of great talks, one epic toboggan race, and nearly unlimited opportunities for networking and discussion. A quick overview of my three favourite talks is below. Check out what you missed and hope to see you in Maine next year! Continue reading “Everything’s Better Down Where It’s Wetter: Benthic Ecology Meeting 2015”

The moral of the story

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Most of us have some inbuilt sense of right and wrong; don’t steal and don’t murder are as basic to us as our ability to breathe. But where does this moral sense come from? In general, people of a scientific bent don’t attribute it to God nor as some sort of free floating truth that can be grasped by the human intellect. If you hold a materialistic view, that is to say the idea that at its base the universe is composed of energy and matter, then it’s next to impossible to understand morality in those terms. Instead the scientific view proposes our morality is an evolved feature, something which gave group-living animals a selective advantage over their amoral competitors. A social group that tries to cooperate when it’s made up primarily of murderers, thieves and cheats won’t get very far. By contrast a crowd of goodies can gain the many benefits of cooperation.

There is a problem with this theory though. Irrespective of its truth, an evolved morality renders us with a situation where there is nothing objectively right or wrong about anything. Even an act of murder isn’t intrinsically immoral. One way to think of this is to compare it with our other adaptations. We don’t consider any other evolved traits ‘moral’, it’s not as if four legs good, two legs bad is something people really espouse. What we’re left with is a moral nihilism.

‘So what?’ you might ask.  We’re a smart species, we can decide for ourselves the best way to act such that our society can flourish. Why don’t we adopt some sort of utilitarianism, the moral system that promotes the greatest happiest for the most, and judge the rightness or wrongness of our acts that way? Indeed this is the way most secular societies establish what is permissible today. This idea can even allow for the expansion of our moral circle to include other beings who are capable of suffering.

Yet the modern understanding of our selves means even a created morality still can’t fairly punish or praise for a simple reason: humans have lost their soul. Modern neuroscience tells us there is no actor in our minds making decisions moral or otherwise. We are our brains, nothing more. There is no ‘I’, no ‘ghost in the machine’. The idea of a freely willed agent who can separate his or her self from their genetics and environment is anathema to anyone who takes materialism seriously.

Much follows from this. Most notably our justice system should be radically re-evaluated in light of this idea to become more biologically informed. Currently persons with certain mental disabilities are afforded more leniency when it comes to their sentencing because they are said not to be in full possession of rational thought processes. Something has affected their ability to have done otherwise. But as automata this is true for every person who has ever existed. This is not to say that we should open up the prisons and free every criminal the world over rather that we should focus much more on promoting environments that cause people to act in a way conducive to a functioning society.

We are all of us robots acting on inputs. Some people take these inputs and act like ‘goodies’ whereas others can take the same information and behave like ‘baddies’. Take your pick of a hero or tyrant from history. They don’t deserve your respect or your contempt. That is the price of a biological morality.

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

Photo credit: http://www.postswitch.de/wp-content/uploads/2012/05/polit-marionetten30.jpg

 

 

Zoological Zodiac

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Aries- March 20 to April 20. Your model will converge around the 13th, which is in no way related to your model convergence dance (turning in a circle three times and raising your left hand twice).  Please stop doing it, we can all see you.

Taurus- April 20 to May 21. A reviewer will suggest additional work prior to publication. Reply to the reviewer with an audio file of yourself singing Bruce Springsteen’s No Surrender and the reviewer will back down.

Gemini- May 21 to June 21. May is a great month for fieldwork. Even if you’ve never done it before and all of your prior research is theoretical, give fieldwork a try. Sure, it’ll be grand!

Cancer. June 21 to July 23. Luck is on your side! This is a great month for finicky experimental work. Optimize your PCR this month and it’ll work at least until June. Probably.

Leo. July 23 to August 23. As Mercury moves into retrograde, your ability to make Powerpoint videos run will be at its peak. Plan an exciting video filled slide show for the 17th. You can make it work this one time!

Virgo- August 23 to Sept. 23. Students in your research group will actually submit work on time. Be prepared for an influx of papers on the 23rd. Assign random grades and see if anyone notices.

Libra- Sept. 23 to October 23. Your research team is going to face an ethical issue within the month. Ask everyone in the department what they think of it and then pick a response out of a hat to solve it!

Scorpio- October 23 to Nov. 22. A research road block will be solved by just ignoring it until the email moves to the second page of your inbox. Go ahead, ignore the issues!

Sagittarius-  Nov. 22 to Dec. 22. News of your ability to comfort sad undergraduates will spread this month. Stock up on Kleenex and sweets in preparation of the post-exam panics.

Capricorn- Dec. 22 to January 20. Someone in the department will steal your lunch twice this month. Try leaving snarky post-it notes. People love those!

Aquarius- January 20 to Feb. 18.  Write a grant application. Please, just write it. Everyone’s waiting on you. Come on.

Pisces- Feb. 18 to March 20. You will be struck with inspiration for a fantastic research project at a conference but then forget it before you can write it down. You should really carry a pen and paper more frequently.

Author: Mystic Mo, william2[at]tcd.ie

Photo credit: http://www.freelogovectors.net/

Productivity!

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A few months ago in our weekly NERD club we ran a session on dealing with stress. Part of this session revolved around what made us stressed, and one of the big problems was feeling like we had too much to do and too little time to do it. To follow up on this, this week we looked at how to be more productive. Many of our discussions revolved around the ideas presented here and here.

What makes us less productive?

The causes of our lack of productivity varied across career stages and the types of work we were involved with. Almost everyone had one major problem – the internet. Postdocs and PIs complained about the huge volume of emails and the desire to deal with them. PhD students weren’t so distracted by emails, instead their issue tended to be things like news websites. All of us have problems with distractions like social media, cute animal pictures and xkcd. Solutions included strictly restricting time doing these things, and/or the number of links you are “allowed” to click and explore before going back to work!

Another big issue was other people. This included supervisors/collaborators who won’t respond to emails or always delay or cut short meetings, suppliers messing up equipment orders, arcane university policies requiring endless form filling, constant interruptions from students etc. This is probably impossible to solve, but did provoke an interesting debate – what if your productivity actually reduces the productivity of someone else? For example, many of us had examples of people who would delay replying to emails until it was convenient for them but this would severely delay someone else working on the project. Another common complaint was people who call you to ask questions – this is great for them as they get an immediate answer but often frustrating for the person who has been interrupted. The only solution we could think of was a) talk to the person involved and calmly explain the problem to see if it can be solved and b) to all think carefully about how our actions affect others (of course I’d like to think we all do this anyway but I know we don’t!)

Finally, we discussed how these distractions all become worse when you have something you really don’t want to do (for me this is grading!). You will do literally anything other than that task. Again this is hard to solve, as it requires self-discipline (and for many people it requires the sound of the deadline whooshing by). My solution has been to work out a really short amount of time that I think I can cope with doing that task for. I then set a timer and do it for that long, or often longer as these things are rarely that bad once you get over the initial hurdle of starting. I then reward myself with a break. I find this works even better if you can do it with a colleague. Yes, it takes far longer to get the task done than it should, but it does get done rather than sitting on your desk and giving you the side-eye all day/week/month.

Unique snowflakes of productivity

An important thing to note throughout these tips is that different things work for different people! I find working at home great for my productivity, others find they spend the whole day tidying the house. I work best in the evenings, other people work best at 6am. Do whatever works for you!

Potential solutions

  1. Be kind to yourself

I think this is most important, especially in light of the stress discussions we had earlier in the year. Most of us are more productive when we eat well, get plenty of sleep, exercise regularly and work sensible hours. Yes, you will get a lot of stuff done if you work crazy hours for a couple of weeks. But that increase in productivity comes at a price of burn out, getting sick or generally losing motivation for the project. Working a 35 hour week has been shown to be most effective for prolonged productivity. Taking breaks is also really important.

  1. Redefine and monitor your productivity

Sometimes our frustrations with how we are doing are related to what we think counts as productivity. We might set goals that are too high, or forget about all the little things we achieved during the day. A suggestion was to make a thorough to-do list (I use trello.com to keep my to-do list synced across multiple computers and because you still get the satisfaction of ticking stuff off!). Making the list is also a useful procrastination activity (see below)! It does make me feel weirdly better when I see small tasks being ticked off, even if the larger whole of the task is yet to be completed.

  1. Find out where your time is going

Another common complaint was coming into work, seemingly working hard all day, but then having nothing to show for it. One suggestion from @DRobcito was to try keeping a “time diary” for a couple of weeks. This involves just noting down somewhere what you’ve done and how long it took you to do it. Although annoying to do, this is a great way to see where your time is going, what you should be spending less time on, and what kinds of activities you might want to say no to in future because the time expended doesn’t match the benefits.

  1. To Pomodoro or not to Pomodoro

A lot of articles on this subject recommend the Pomodoro technique where you work for 25 minutes, take a short break, then work another 25 minutes. After four or five repeats you take a longer break. Most of us had tried this, or a version of it, and most of us found it didn’t work for us. I think this may be related to it being hard to get anything sensible done in 25 minutes when analysing data or writing a paper. But as mentioned above, I often use something similar when grading papers which works really well.

  1. Have a “me” day

This is perhaps more for people later in the their careers, but it’s good to have one day a week where you don’t do anything for anyone else, and you don’t go to any meetings. You only do things that will add to your CV. Essentially this means working on papers or grants. Maybe not such a big deal for PhD students, but I can definitely go for weeks without working on any of my research. Another thing to avoid on these days is admin and non-essential emailing.

  1. Procrastinate effectively

Instead of watching a video of a capybara bathing with ducklings during a break, move on to something that requires zero intellect, but still requires doing for your work, for example reconciling expenses/receipts after a trip, formatting references, playing with figures, searching for new literature etc. Having said that, it’s important to also take proper breaks, and to ensure you see the capybara video.

  1. More efficient meetings

Another suggestion from @DRobcito was to have 22 minute meetings. We were dubious about this but he claims it works, mostly because you have to cut to the chase immediately. He also suggested scheduling back-to-back meetings to prevent any of them from running over. Again this doesn’t always work and can just lead to all your meetings starting late which may be great for you but is unfairly detrimental to the productivity of the people waiting for you.

  1. Dealing with emails I

A number of people use the “5 sentence max” email rule to keep emails short and to the point. If an email needs to be longer you should Skype or meet in person. We decided this works sometimes but not others. Many of us like to have details on email rather than talking them through on Skype or in person. Additionally, some of us really hate the trend of really short email replies because it’s hard to gauge tone, and also it seems a bit rude not to address the email to a person. This may be a cultural thing.

  1. Dealing with emails II

Most of us can’t get much done without internet, so turning off the internet wasn’t an option. But we can all turn off our email notifications on our phones, tablets and computers. This prevents you from dealing with the emails as the come in, but also removes the distraction of the notification itself which can break your concentration. Different people had different strategies for emails. Some do emails in set blocks of time, others do them during breaks. I think in terms of not injuring other people’s productivity it’s probably polite to at least triage your email in the morning and sometime in the afternoon. I also use the rule that if I can respond to the email/do what it asks me to do in less that 5 minutes, I do it then rather than leaving it to fester in my inbox.

  1. Manage your time, energy and attention.

This article explains this in more detail. Essentially, being productive requires that you have time to work, the energy to work, and the attention to work. Even if you have an hour to work on a paper, you still won’t be productive if you’re too tired to do anything useful or keep getting distracted. All of the above are solutions to one or more of these issues.

Author

Natalie Cooper @nhcooper123

Thanks to @DRobcito, @jonesor and @naubinhorth who helped with suggestions for our discussions.

Photo credit

wikimedia commons

No time like the pheasant

 

Let’s run another photo competition. Starting today and running until Monday 18th May anyone can submit one photograph to this album here. Just log in with username ecoevoblog and password is the same. Don’t make it obvious that it’s your image in case it biases the judge. The theme for this month will be ‘Fowl Play’. Prizes will be determined in due course.

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

Photo credit: https://commons.wikimedia.org/wiki/Aves#/media/File:Tauraco_hartlaubi-20081223b.jpg