MetaEvoPhyloEcoOmics is moving

MetaEvoPhyloEcoOmics is moving to a new blogging platform. The main reason is I want to post more about R coding, and I use a lot of MarkDown, so I want a blogging platform that has good support for this. So I am moving to the awesome new blogging platform Ghost. I have a preview version of the website up already at Once it is fully up and running I will transfer my domain name over so I will still be at

And it looks a lot nicer I think! I am using a theme styled after the awesome writing site Medium. You should check Medium out too. I think it has a lot of potential for science blogging, but it hasn't caught on yet amongst scientists.

See you on the other side!

Sounds, Trees, and Models of Life - Weekly WHOMP -

This will be a short Wednesday Hyperlinks Of My Preference, but there were a few cool things I'd like to share this week. I will be posting some actually substantive articles soon! In the mean time, check these sites out!

  • Nature Soundmap: This is one of my new favourite websites. I suspect this will remain a favourite and be visited many times by this listener in the near future. A map of the world on which is placed nature recordings from all sorts of habitats. I love nature recordings; they are my favourite thing to listen to while I work. Some people like music, but I find it too distracting. The sounds of nature always make me feel more relaxed, and here is a whole world of them.
  • OneZoom, Tree of Life Explorer: A fantastic way to visualize the relationships between all life on Earth. Zoom in and out of a massive fractal structure upon which is mapped our fellow species as well as ourselves. Try and find the Homo sapiens lineage by zooming all the way in. Gives you a humbling experience of our place in nature (and this is just on the Tetrapod tree!), in a similar way to how seeing the earth's position in the milky way gives us proper perspective on our place in the universe. Only a few trees up right now but this will be especially cool once more people put their trees on it and get them connected up. You can even embed a tree. Click below to zoom to humanity!
  • The Madingley Model of Life on Earth: A great idea whose development I will be watching closely. This is an attempt to create an ecological simulation that can model all of life on Earth. There is still much to be done, but I think this is an impressive start. Only time will tell how complex simulations such as this will aid our understanding of ecology and inform our policy in regards to protecting and maintaining ecosystems, but we will never know unless we try. Fortune favours the bold, as they say, and this project is nothing if not bold. Which is what I like about it. And, the code has been made available entirely open source, which is fantastic. My hearty thanks and congratulations to the team behind the Madingley model. I would love if this could be the base of a global open source software collaboration between computation ecologists around the world. Something like the R or the Mozilla Firefox, or perhaps Ubuntu of ecological simulators, that is, if we can get enough ecologists to agree on what should go in. 

To summarize, three examples of a global, cooperative projects that give us some perspective of life across the Earth and our own place in all of its chaotic wonder.

    Eusocial Media? (+ WHOMP)

    Eusocial Media?

    This week I read a really interesting article by Joe Dramiga about how we can model social media trends in a similar way to how we might model ants, as they leave their pheromone trails. You Inner Ant: How Popularity on the Web Arises by Trial and Error makes an analogy between the trail-laying and trail-following behaviour of ants foraging for food, and the link-laying and link-following behaviours of human beings browsing the web. I can surely see the similarities: ants move randomly away from their nests, while laying a pheromone trail. When they find food they return to the nest and then use their own trail again to get back to the food, reinforcing the trail. Other ants that stumble across this trail will follow it, and reinforce the trail even more. Soon this trail will be stronger than any other trail and so most of the ants in the vicinity will use it until the food source is used up. In humans, a lucky person will be the first to discover some cool new website, or start following a really interesting new twitter user. They will leave an 'internet trail' of links and social media posts that are followed by others, who in turn reinforce the trail by leaving their own links and posts pointing to the same 'internet food' source. Really cool idea!

    The idea breaks down somewhat with the discussion of how this leads ants to find the 'shortest path'. According to the article, the first ant to find the food has the trail that is the most likely to become popular (because it has had more time to be found and reinforced), and the first ant to find the food must also have taken the shortest path (because she got their first), meaning that the most popular trail should also be the shortest trail most of the time. Side-track: However, this only actually guarantees the shortest path out of all the paths that were tried within some time-frame. An ant that took a shorter path but left later than than another ant with a more convoluted path may be too late for her path to 'catch-on'. In other words, a 'priority + positive feedback' effect has caused a sub-optimal path to become popular! If a certain proportion of ants leave the trail they are on to explore side-paths, this would eventually refine the path to the shortest path. Likewise, if another trail is substantially shorter, the amount of time to move up and down it is shorter, and thus will be reinforced more frequently, leading it to eventually overtake the first trail in strength. I assume some of this does happen with ants (I don't know the ant literature that well!), and that the article was just trying to keep it simple by not discussing this. In any case, it is unclear how 'shortest path' applies to the social media example because generally people who lay down an 'internet trail' simply lay down a direct link to the 'internet food' without reproducing their potentially convoluted trail to get there. 

    Are there Hipster Ants?

    I would also say, the ants presumably use trail-laying and trail-following at least in part because natural selection has "discovered" that this is an efficient approach for maximizing the benefit to the whole ant colony. In the social media example, it is not clear to whom this behaviour is beneficial, if it even is beneficial. It certainly hasn't emerged because it is beneficial to society at large.  Because of this, there is no reason, once it has found a food-source or a trail to one, why an ant would want to abandon that food source until it is used up. On the other hand, there are people who will actually avoid following a trail because it is being used a lot---the opposite of the ants general behaviour. It makes me wonder if their are, in fact, a kind of hipster ant, which avoids strong trails in favour of forging their own. I could see how a few ants that did this in a colony might make the whole colony better. Maybe someone who knows something about ants could enlighten me on this?

    For this reason I am not sure if the article's suggestion that human social media data can be used to help understand ant social behaviour will pan out. But I would love to be proved wrong, because that is some cool 'internet food' for thought. Please follow the internet trail I've just laid down and check out You Inner Ant: How Popularity on the Web Arises by Trial and Error.

    Some more Wednesday Hyperlinks Of My Preference

    Slow Life

    This is an absolutely amazing timelapse video of corals going about their inscrutable and beautiful business.

    Here is my animated GIF which I have also titled "Slow Life" or "Snail on a Cycad: That's Pretty Slow"


    I am a bit late to discover this but I thought it was cool nonetheless. Phylo (Kawrykow et al. 2012) is an online puzzle game in which the goal is to align sequences of coloured 'bricks' in different rows together into columns so that they match as closely as possible. This sounds like your generic 'tetris-style' (or even better 'puyo-puyo'-style!) puzzle game so far, but what is cool is that this game-playing is fueling the search for better phylogenies. Because it turns out that alignment of DNA sequences is still more accurate when done by eye than by the most advanced computer algorithms. That's right the coloured bricks actually represent DNA base-pairs and the sequences you receive in the game are from actual organisms! When you play this game, you become a node in a distributed massive parallel computer, made up of human minds. And, the craziest part is: this game is actually fun!

    Warning: This game could be particularly dangerous for biologists who are prone to distraction, such as myself. I call this a 'wolf in sheep's clothing', because it is too easy for me to justify playing this game as a biologist---after all, it is sequence alignment. I have to align sequences all the time, surely this is just good practice? And this is contributing to science, and, as a scientist, I therefore would be doing my job by playing this game. In fact, if I didn't play this game, surely that would be a disservice to science! And so on. So for those of you who feel the allure of the Dark Playground, be careful with this.

    The only issue which might make it less fun as time goes on is that it is possible to get stuck on an impossible level. Because the game uses real unaligned sequences, there is no way for the game to know what the highest possible alignment score is. Therefore, sometimes the score required to get to the next level is higher than is actually possible.

    Check out the paper describing it:

    Kawrykow A, Roumanis G, Kam A, Kwak D, Leung C, Wu C, Zarour E, Phylo Players, Sarmenta L, Blanchette M, Waldispühl J (2012) Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment. PLoS ONE 7(3): e31362. doi:10.1371/journal.pone.0031362

    Natural History TidBit(e) from Borneo - The story (literally) of a bloodsucker.

    Last month my wife and I made an unforgettable trip to Malaysian Borneo, to Mount Kinabalu and vicinity.

    It was our second time to Borneo, and will not be our last. In our mind's eye a mist seems to arise from this island, with luring tendrils that tug gently at our imaginations (like the animated smell of a pie in a saturday morning cartoon). It is truly a paradise for the natural history nerd. Smothered by biodiversity, we strolled through rainforest with dazed delight. All the way, snapping photos with our relatively inexpensive camera.

    I plan to do a series of posts showcasing some of these photos. A photo journal for each of our natural history hikes. This is the first short one.

    Here, I want to tell you about a wonderful retched creature. Because if you wish to gain entry to the green-cloaked hallways of the Borneo rainforest, you must pay a toll -- one of blood. A story:

    A sucker meets the slick surface of a leaf, and holds. Reaching out again, stretching elastic muscles for the next grip. Emerging from damp earthen debris, where the dry does not venture. Rain equalizes, and makes the light as water-laden as the darkness. Hunger draws us out. And now there is a shimmering wave of heat ahead. It is large, an amorphous radiation of heat, a vibration of movement. Of blood. Hunger draws us on. Light turns to dark -- it is close! Reach out a wavering tentacle, all of ourself, looking for a brief connection, enough to hang on, unnoticed, one with our prey. Sucker meets warmth, and we are away. Flesh yields to rasping teeth and sustenance flows. Soon to be engorged, satiated, to live another day. The damp earth entices again. It is time to flee the sun, as the moisture flees it, until the next rain. Until blood is carried past again. 

    We are a terrestrial leech, a common denizen of the Northern Borneo rainforest. Unlike the leaches that most people are familiar with, which are primarily aquatic, these leeches are perfectly at home on land. They are still at risk of drying out, but the rainforest is wet enough that they can be quite active during the day, especially after it rains. They tend to climb up on vegetation and stretch themselves out into an opening such as a hiking trail, and wave wildly, trying to attach to anything that might pass. This was the first terrestrial leech we saw, a Tiger Leech (Haemadipsa picta):

    The second one we saw was attached to my leg (and the third, and the fourth, ...):

    This one is the other species of terrestrial leech that occurs here: the Brown Leech (Haemadipsa zeylanica). Once they are fully engorged the leach will drop off and return to a damp, dark place to digest and take shelter from the drying heat of the sun. The bite can be felt, and for me was quite uncomfortable; the bites are still itching slightly right now, more than a month later. Apparently, the idea that leeches secrete an anesthetic in their saliva (to be sneaky) is nothing more than a myth. They do secrete a chemical that acts as a blood-thinner and inhibits clotting, however, as I soon found out.

    The aftermath of a leech. I hear it is much worse if you do not let the leech finish its business and drop off naturally.

    More leech handiwork, bloodstains. 

    Unfortunately, we didn't encounter the coolest terrestrial leech on Mount Kinabalu: the endemic Kinabalu Giant Red Leech.

    Video by Ian Hall.

    These leeches are huge (up to 30 cm!). Luckily they don't feed on mammals but rather other invertebrates, including the Kinabalu Giant Earthworm.

    Borneo, can you get any cooler?

    The first weekly Wednesday Hyperlinks Of My Preference (WHOMP). Popular Science Links, and Useful Writing Tools

    It is Wednesday Hyperlinks Of My Preference time, for the first time.

    Here are some of the links around the webs I found interesting or useful. Let's WHOMP.

    Popular Science

    Some of my favourite popular science writing from last week:

    • The Worst Places To Get Stung By A Bee: Nostril, Lip, Penis - By Ed Yong. The story of a very dedicated scientist out to answer the burning (make that stinging) question of where is the most painful place to be stung. The target audience appears to be humans but this information would be very valuable for angry bees. Let's try and keep this from falling into the wrong tarsi.

    Useful Tools

    Here are two online writing tools that may help you if you are writing a paper or a thesis chapter. I think both of these have great potential but neither quite have all the features to make them a killer app just yet. Using the cloud to do writing has many advantages, including automatic backup, the ability to work on a document from anywhere, and ease of collaboration and sharing of the final result. 

    Both of these tools are primarily based on markdown, and could be a good way for anyone who is thinking of picking it up to give it a try in a nice looking GUI system. If you don't know what markdown is, @_inundata has some good resources here. Also, @polesasunder has an interesting post on a small part of his experience with markdown (I promise you, it is not just for hipsters). Here are a few pros and cons of what I think are the two most promising cloud writing apps I've tried.



    • Version control using Git (awesome!) 
    • Easily rearrange paragraph order
    • Automatic citation and bibliography generation by simply pasting DOI numbers into the text (Love this feature!) 
    • Integration with iPython Notebooks for on the fly or interactive visualization 
    • Writing with either markdown or Latex
    • Unlimited public documents. Free for papers being published open access (Love this!) 


    • Only one private document with a free account; you have to pay for more. 
    • Interface not keyboard friendly, which makes it a bit clunky. 
    • Limited export formats (just PDF, markdown and Latex), no Word export could be a deal breaker for some people.
    • Most importantly for me now, no R integration (they say they are working on it!). 

    Overall, once R integration is achieved this could make me think about switching from my current solution using RStudio with rmarkdown, and GitHub for syncing and version control. More about this system in upcoming posts!

    Gingko App

    This is still in early beta and has much fewer features than Authorea at the moment, but what makes it stand out is its delightful fluidity.


    • Incredibly elegant, everything can be done with the keyboard without any complicated hotkeys to remember. 
    • Fully hierarchical structure that unfolds across the page, allowing you to outline and write your content in the same place. They call it tree-based word processing. It is quite stunning.
    • Styling with markdown and Latex. 
    • Export to useful formats including markdown, PDF, html, and importantly Word. 
    • This video shows some of these nice features:


    • Adding figures is not simple as you need the image to already be online and have a URL 
    • No automatic citation system yet (they say they are working on it).
    • Free account is limited to only three documents (which they call trees), for more you must pay

    Overall, I love this app, and I think once I got the hang of it, it could be that rare software tool that actually aids the flow of ideas, rather than disrupting them. For now it is great for the early stages of writing where you are trying get the structure down, but it also lets you add in content as you go, so you can go wherever your mind takes you. Perhaps after this stage, the document can be exported to another program for the finishing touches such as citations. 

    Both apps allow multiple users to work on a document at the same time, so they are both fantastic for collaboration. To summarize, Authorea has great technical sophistication and some real sweet features, but a somewhat clunky interface (but its still not bad at all), whereas Gingko App makes up for its lack of bells and whistles with elegant simplicity. I am looking forward to see whether the upcoming planned features for these apps will make one of them the killer writing app I've always been looking for. I hope you give these a try, because I want these tools to be a success and have the chance to reach their full potential.

    A new blog is born. What the!? Its slimy!

    Welcome to my blog MetaEvoPhyloEcoOmics, or MEPHEO for short. I debated long and circularly about whether I would make my first post an introduction – like this one – or just dive right in with a regular post. I decided to do this to introduce some of the features I'd like to have on this blog, and therefore light a proverbial fire (using proverbial hypertext matches of course) under myself to get some posts actually written.  The main purpose of this blog will be to talk about issues in the science of ecology, and science more generally, and to form part of an open lab notebook for my research (along with GitHub, Figshare, etc.). 

    I am an ecologist, currently working for CSIRO as a post-doc, in Perth, Western Australia. All the opinions I express here are of course my own (yay! now this blog is in compliance with my company's social media policy!) . There is more info about me available on the left sidebar, should you be interested.

    I have two regular features planned for this blog that will be interspersed with ecology and science posts, and one experiment I'd like to try.

    Regular Features
    • Weekly links, with commentary! This is a common thing to be found on blogs, and this one is no exception. Friday is often the day these link dumps occur, but I am going to do mine on Wednesdays (yes that means tomorrow is the first one!). It is hump day and so this is the day I most need to take a break from work and prepare my mind for the next half of the week. What am I going to call it? Well, "Wednesday Hyperlinks Of My Preference", a not-at-all awkward phrase whose acronym happens to be WHOMP! So from now on hump day is whomp day here at Mepheo.
    • A weekly or bi-weekly feature called "Photography with a Relatively Inexpensive Camera". One of my hobbies is capturing images of natural history and other interesting science things, but I have not yet succumbed to the siren call of an expensive DSLR (or is that the hum of the auto-focus?). I do have a water-proof and shock-proof point and shoot camera, with which I do the best I can. It has a macro mode, which is good enough for me. To make up for low image quality, I try and do some more interesting things with the photos, including post processing. By the way, in case you were wondering, though I myself don't care for them, the acronym for this feature is PHWARIC (which I assume is pronounced "fwaaaaaaaa!... rick"). Some of these photos may have been taken by my wife as well. Any image that appears on this website will either be produced by me, or have full attribution to the creator whenever possible. If you ever notice me slip in this regard, please do call me on it.

    Experimental Feature

    Much of what I do as an scientist is to analyze data, usually collected by other people. That's right, I am a data parasite (the first step is admitting you are a parasite). But haven't you always wanted to know how parasites make their living? To experience it from their perspective as they wriggle and squirm their way through oozing piles of other people's data? Well, now you can find out. The idea is that I am going to go through the process of taking several public datasets, analyzing them (with R and GitHub), and hopefully turning that into a (open access) paper down the line. I will post every step along the way here, and invite comments from the online community. I am looking for this to be a kind of crowd-sourced online collaboration (complete with coauthorship), with whoever wants to chime in. Hopefully I can get enough people interested! Even preliminary analysis will be public, so it is entirely possible the project will fizzle before it even gets started if the dataset is not up to the challenge. We will all see together.   

    I will advertise this again once I have decided on a dataset and a problem to work on. It will almost certainly involve phylogenies and probably GBIF data! I would of course welcome any suggestions for cool datasets and questions to ask on here. If anyone is reading this and likes the idea, or knows of someone who has already done something like this, please leave a comment, or tweet at me (@ecologician). 

    I will leave you with a natural history animated gif, of a nest of bees my wife and I discovered while hiking on an offshore island near Kota Kinabalu in Malaysian Borneo. It may take a few minutes to load. Taken with my relatively inexpensive camera.

    Acronyms used in this post:

    • MEPHEO - MetaEvoPhyloEcoOmics
    • CSIRO - Commonwealth Scientific and Industrial Research Organization
    • WHOMP - Wednesday Hyperlinks Of My Preference
    • PHWARIC - Photography With A Relatively Inexpensive Camera
    • TBDLLB -The Blog is Dead, Long Live the Blog