MetaEvoPhyloEcoOmics

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?

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"

Phylo-gaming

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

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:

• Trilobite Beetles are Happy Being on Land, Alive in the Present Day - By Bec Crew. This is an article about a really cool genus of beetles known as Trilobite Beetles (Duliticola). I am a big fan of arthropods in general but these are extra cool because sexual dimorphic pedomorphosis! That is the females retain juvenile (larval) characteristics into adulthood, which is why they don't really look like beetles.

  
  By Dave.Dunford (Own work) [CC-BY-SA-3.0], via Wikimedia Commons

• 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.

Authorea

Pros: 

• 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!) 

Cons: 

• 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.

Pros:

• 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:

Cons: 

• 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.