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 mepheo.ghost.io. Once it is fully up and running I will transfer my domain name over so I will still be at mepheoscience.com.
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!
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.
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.
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
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, ...):
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?
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.
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.
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.
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.
Pros:
Cons:
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!
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:
Cons:
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.
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.
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:
