Saturday, November 23, 2013

Writing the self-contained universe

You are not sitting next to me right now as I type these ideas. You're most likely not in New Jersey, and you might not even be in the U.S. The fact that it's even possible for you to be reading these words right now highlights an ever-growing need to be able to communicate ideas through writing. It's the difference between you growing bored and leaving halfway to explore other parts of the internet, and you finishing this blog post (before moving on to explore the rest of the internet!).

In essence, writing is just a means of getting info from Point A to Point B. No matter how many amazing and intelligent ideas you may have in your head, they will have to stay there if you don't know how to communicate them. Here are a few tips on bridging the gap between you and your reader's mind when it comes to e-mailing a professor or potential collaborator, writing a grant, or explaining your ideas in general. 

1. Who is your reader? Why should they care about your message?
Example: e-mail
As often as possible, put yourself in the head of the person reading what you wrote. Let's say you're e-mailing a professor to potentially do a PhD with them. They'll want to know:

- Who is this person? Is he/she currently an undergraduate? If not, what has she done since then?
- What are his research interests? Of my work, what interests him?
- What are her research qualifications? Has she done research before, or is she just applying to grad school because she hasn't considered other options?
- Has this applicant actually read up about my lab and thinks he's a good fit, or is he just sending a template e-mail to every researcher he can find?

The more of these you can answer, the more willing the professor will be to respond. Remember that professors are incredibly busy people. Chances are, they enjoy talking with new people and exchanging ideas. But, their schedules are so packed that the easier you can make an e-mail exchange for them, the less time they have to spend answering these questions themselves. You want a researcher to be nodding her head as she reads the e-mail, her questions being answered as she reads so that by the end, the work has been done for her and she can now focus on writing her response.

2. Does your writing actually address what you wanted to say / the prompt?
Example: grant writing, lab reports
Say you're working on an NSF-GRFP grant (the National Science Foundation Graduate Research Fellowship). You have phenomenal research ideas that would explain a genetic basis for sociability in humans, and you have told a heartwarming story on how you discovered and decided to pursue science. A few months later, you're surprised to find your revolutionary ideas were not funded by NSF. What happened?

It's likely that you didn't answer every part of the application to the degree NSF was looking for. Consider an introductory biology lab in which the students dissect fish and chicken hearts (diagrams on the right). In their report, they are asked to compare the two hearts and explain how these hearts differ in the ability to support different levels of metabolic demand. Unless they provide comparisons between the two hearts and explain how those differences affect ability to support varying metabolisms, they will not get full credit (no matter how detailed either component of their answers are). Think of it as:

1o points total:
5 - provide 3 differences between the 2 hearts
5 - explain each difference in terms of metabolic potential

You can slam dunk those first 5 points, but if you don't address the second section, it's likely you won't even get a passing grade. Similarly, for the GRFP, regardless of how incredible your ideas are, if you don't explain how your work has any relevance outside of bullet points in a textbook only people in your field will read, even the very best ideas will get passed down. Again, think from the GRFP officer's viewpoint: every applicant has good ideas, but NSF wants research fellows who will not only advance science but also help spread its ideas beyond the scientific sphere. Even if you would do outreach if you had the opportunity, if you don't write about it, the GRFP officer can't assume you would.

3. If your writing was an isolated universe, would that universe make sense?
Example: course exam
This is one I repeatedly tell my introductory biology students for their lab reports and exams. Imagine your mom somehow stumbled across your biology midterm essays (of all the things she could have discovered in your room) and was reading them. Would she be able to understand what you wrote? In this situation, you have someone who most likely hasn't taken college-level biology in a few decades, if ever. Do they get lost in your jargon, or is your answer self-contained enough for anyone to be able to pick it up and learn something from it? One of the biggest road blocks to a good scientific talk is losing your audience part way because you assume they understand something they actually don't. Being able to grab a listener from any background and pull them to a new level of understanding is challenging, but it's critical for teaching.

4. How long do you think your reader will spend on your writing? If they skimmed it, would they still get your message?
Example: lab report, scientific articles
Many science majors in college are under the misconception that a longer lab report is a better one. The idea, which seems reasonable at first, is that the more information you put down, the larger the net you are casting, which has a better chance of catching the answer your TA is looking for. Unfortunately, it's not quite like that. Aside from giving yourself more opportunities to write something incorrect and actually lose points, in the scientific world you will almost never be in the situation where you've written everything you need and should keep writing more.

Again, think about writing as a communication of ideas. Short and sweet (i.e. efficient) is always preferable to long and winding in science. Scientific articles have abstracts so readers can get the gist of the article without needing the motivation, background, and time to read the entire thing (remember how busy many researchers are!). Articles in the journal Science actually have one-sentence summaries for the particularly busy and researchers in related fields who may want a simplified version of the abstract. Brevity is a much better skill to have than the ability to list everything you know about a topic.

Consider the reader, consider your miniature universe. And if all else fails, just call your reader on Skype.

Photo credits:
- Thinking: Basic College English blog (
- Chicken heart: University of Illinois at Urbana-Champaign Chickscope (
- Fish heart: Stanford University Environmental Science Investigation (

Saturday, October 5, 2013

Monuments - "Regenerate"

Layered with guitars and powered by tightly-knit bass guitar and drums, "Regenerate" by the progressive metal / djent band Monuments is a song of epic crescendos and releases. I discovered the song randomly through related videos on YouTube and it's one of my favorite songs now.

Artist: Monuments
Song: "Regenerate"
Vocals: Clean, growled

The music video:

A drum cover I did (with a drums-only version at the end):

(Time stamps are from the music video.)
0:00 - 0:49
The song begins with a bass note fading into silence, the remnants of a conflict that played out in the previous song disappearing into the distance. An eerie guitar strikes clear notes whose spaces fill with echoes, the persistent beams of a lighthouse blurring as the fog rolls in, or the light from a torch struggling to fight the darkness of an enormous underground cavern. The bass and drums enter, setting the track in motion and beginning to build tension. The drums do this by first opening the hi-hat on the snare hits to accent those notes, and then gradually opening the hi-hat throughout the second half until it's fully open (and loud and noisy). Then, riding the crash cymbal and headbanging, of course.

0:50 - 1:17 (6:23 in drums-only version)
Chaos. The bass drums here are hard-hitting, a pattern that alternates between a short roll that ends on the left foot (if you start on the right) vs. a long roll that is three notes longer, ending on the right. It'll look like R-L-R-L --- R-L-R-L-R-L-R --- R-L-R-L-R-L-R --- R-L-R-L --- and so on. At the end of the measure, the bass pattern continues into the second measure, restarting the pattern. That last bit looks like R-L-R-L-|-R-L-R-L, where the | signifies the transition into the next measure (though it's continuous, with no audible break).

1:18 -  1:44
Ascension into beings beyond the present form. The lyrics here:

                                           Free from my bonds
                                              No longer alone
                                        Never born, will never die
                                           No need for crowns
                                        We wear the stars now

The drums are super fun to play at this part, with the left hand throwing in hits on the splash cymbals while the feet maintain another hard-hitting rhythm.

1:45 - 2:12
The build-up to one of my top three favorite progressive metal riffs. I love how elements are progressively added, continually building the intensity.
- 1:45 - Guitar: angry, electric; drums and bass setting the foundations. Calm vocals
- 1:52 - Background guitar: memories flitting to the forefront of consciousness before slowly disappearing back into the murky water
- 1:59 - Background guitar: the memories grow louder, more prominent
- 2:04 - Vocals: as he sings "And we all believe, knowing we belong," a guitar starts in the background, a bundle of electric thoughts tinged with longing and suppressed energy that continues to grow in intensity. It's the start of an idea, a seed, the thought that the way things are right now isn't necessarily how they should be.

2:13 - 2:39
That bundle of thoughts now shoots forth to the front of your mind, exploding fully expressed. Meanwhile, the background guitar introduced at 1:52 continues, memories of a face, the outlines of the jaw and the nose but the eyes still dark and unreachable, sliding to the front of your mind's eye but disappearing before you can get a close look, like a leaf in the wind. The vocals progressively build in urgency and emotion before the cathartic growl/shout at 2:30. I haven't been able to find the lyrics for this section anywhere (including the album booklet when you buy it on iTunes), but I think he's saying something between "the red leaves fall," and "the reach seems far." Side note: the bassist's giddy face in the background is a pretty funny contrast to the intensity of the vocalist growling at 2:35 and 2:38.

2:40 - 3:08 (8:13 in drums-only version)
Calming down from that enormous rush in the previous section. Seasons passing, the heat of summer giving way to autumn and winter. I envision villagers in a Lord of the Rings-esque world, their homes burnt down by ravenous orcs and the only direction to move is forward, to let time heal the anger and loss.

There are two ways to do the drum pattern in this section if you want to have a roll on the snare as well as keeping eighth notes for the rest of the band to stay on time. The first way is to use both hands on the snare (easy) and use your left foot to keep time on the hi-hat (fairly hard because you have to disassociate it from your right foot). The second way is to have one hand keeping time on the hi-hat or ride (easy) and to do the entire drum roll with one hand (easy if you've done marching band, hard if you haven't). I did neither... I used both hands for the snare roll. This is why I drum on the internet and not in front of thousands of screaming fans, unlike Luke Holland. (Side note: I'm looking away from the camera in this part because even with the riff dumbed down, I still had to concentrate quite a bit to get the accents right on this section).

3:09 - 3:35
Nothing's ever been this clear
No one needs to feel alone
And the change is set to seed
But we need to take this new form

Love is truly here
We just need to let it breathe
We have glimpsed a new aporia
In the moonlight of our gnosis

3:36 - 4:05 
The apex of the song. I love the vocalist's extended growls here.

4:06 - 4:30 (9:39 in drums-only version)
A modified version of the drum beat from 1:18 (with more splash cymbals!). 4:16 is interesting because the drums do a fill to indicate the end of a measure, but then the end of the guitar riff follows a few seconds later, at 4:18, after which the whole band starts a new riff. This is probably a (cool) artifact of trying to fit riffs into clear-cut boxes of time signatures.

4:31 - 5:39
Outro. The drums alternate between a normal rhythm and a slightly delayed rhythm, where there's some space between the snare hits. When learning this song, I literally memorized it as "2 delayed, 1 normal, 1 normal to delayed, 1 delayed, 3 normal, 1 delayed." The drum cover at this section actually produces a cool effect: while previously my drums were nestled within the song (and Monuments' drummer's playing), the fade-out of song audio brings my drums to the front. This is cool because in YouTube drumming, it's extremely common (and I'm victim to this too) to hide your drums in the audio of the song, because then you can worry less about getting the song 100% correct as well as being perfectly synchronized with the band. Showing your actual playing is a bit of a statement that, yes, I really am playing the drums under all the music, which is one reason I always include a drums-only version of my covers. (Other reasons include that I love hearing the instrumental and drums-only versions of songs, and it's much easier to learn a song if you don't have to tune out the other instruments.) Another reason I think it's cool is that it's like you've become an audio engineer, able to adjust the volumes of different instruments. 

Amazing song! I'm not as huge a fan of the rest of the album, but I'll be listening to this song for many years to come.

All images taken from the music video and Gnosis album artwork belong to Century Media.

Tuesday, September 10, 2013

Problems with adaptationism

While the basics of evolution are relatively easy to understand, the finer details are surprisingly convoluted. A big debate in the second half of the 20th century concerned adaptationism, or the belief that every trait we observe - be it morphological or behavioral - was specifically selected for and has an adaptive explanation for its existence. Adaptationism argues that natural selection is the only significant means of evolution (the others being genetic drift, gene flow, and mutation), which means that if a trait exists, it is the optimal solution for some question behind it. The debate technically isn't over, with big-name researchers like Richard Dawkins and Steven Pinker still arguing for adaptationism. While many traits in an organism clearly are the result of natural selection, this blog post will highlight problems with trying to extend this thinking to everything you see in an organism.

The beginnings of adaptationism
The groundwork for the debate began with the publishing of two tremendous books, E.O. Wilson's Sociobiology: The New Synthesis (1975) and Richard Dawkins' The Selfish Gene (1976). Sociobiology attempts to explain social behaviors through an evolutionary lens (e.g. how does an animal's aggression lead to it having more offspring in the next generation?). The Selfish Gene is an argument for genes being the unit of evolutionary selection; in a survival of the fittest billions of years ago, a gene that could produce more copies of itself inevitably outcompeted all other variants. (It's quite a bit more complicated now.) 

Big problems arose when researchers began interpreting human social behavior using Dawkins' reasoning for the evolution of genes. These people, who started being called adaptationists, began claiming that any human behavior you see today - cutting someone off while in traffic, some women preferring taller men, smiling when we're happy - had a story behind it. Any human behavior... including suicide, necrophilia, child molestation, torture... had to be there because our ancestors who didn't perform those behaviors were outcompeted by those who did. 

Unraveling the logical missteps
Stephen J. Gould and Richard Lewontin took the first big stab against adaptationism in 1979 when they published a paper critiquing evolutionary biologists for the following four problems:

     1. Relying on story-telling explanations that are impossible to scientifically test

     2. Overlooking other methods of evolution besides natural selection

     3. Overlooking evolutionary and physiological trade-offs and constraints

     4. Claiming that the current way a trait is used is the reason it originated

Let's explain these in simpler terms. A lot of adaptationism utilizes just-so stories. A just-so story, also called an ad hoc fallacy, is an unverifiable explanation for how a behavior or morphology came to exist. It can't be proved or disproved; it's basically the opposite of hypothesis testing because you're looking at the results of something and then forming a question that leads to your answer.

Here's an example of this flawed reasoning. Say you're doing a census of fox populations in the wild and in the city. Interestingly, you notice that foxes in the wild tend to be orange while city foxes are generally a mix of gray and orange. You conclude that foxes in the city have evolved orange-gray fur as a means of camouflage in their predominantly gray landscapes.

Slow down a minute. Yes, this is one potential explanation for what you've seen, but you can't rule out dozens of other equally-valid explanations that have nothing to do with adaptation to the city. What if the genes for fur color are closely associated with genes for neophobia (fear of novelty), and as less neophobic foxes outcompete their more novelty-fearing conspecifics, their fur color gets dragged along as well? What if foxes in cities actually represent a small founding group isolated from groups in the forest, and their gray fur just happened to arise due to genetic drift? And depending on whether you actually handled any of the foxes in your census... what if the gray foxes were just dirty? (Yes, sometimes an explanation this silly has to be considered if your methodology didn't control for it.)

The problem with adaptationism is that you start viewing organisms as a bundle of optimal traits independent from one another. In reality, there are a lot of evolutionary limitations and trade-offs within an organism. For example, zebras don't have machine guns because machine guns were not available as an ancestral trait to be selected for. Similarly, organisms are subject to constraints within themselves. Even though our muscles, bones, and digestive organs don't really do anything to make babies (the only thing that matters from an evolutionary perspective), humans are not huge ovaries and testes running around because we need the other organs to acquire resources, not get eaten, and then get to the point of reproducing. (It's probably for the better, though life would be a lot more entertaining.)

In the example above, you can't test a hypothesis on why dogs have floppy ears. Even if you were to conduct an experiment with lots of carnivore species with floppy ears and somehow found that yes, floppy ears really do help divert water, you still wouldn't be able to say whether that is why floppy ears came to be. One alternate equally-untestable explanation could be that floppy ears were developed to look cute, but then dogs started using them to divert water to the ground. The possibility of a trait developing for one reason and then being used for another is well established; a great example is that insect wings probably originated as a means of thermoregulation.

A case study: human rape
The human implications of Dawkins and Wilson's work spawned enormous controversies, particularly with the eugenics of the Holocaust still fresh in everyone's minds. If every behavior had an evolutionary reason behind it, could we really be blamed for anything we did (i.e.  genetic determinism)? What was stopping the government from rounding up people who behaved a certain way and sterilizing them? At what point would the interpretations of the science start being bent by powerful groups of people trying to control other peoples?

By adaptationist logic, men brutally raping women is an evolutionary adaptation to ensure our genes get passed on. Even today, some people really believe that the tendency to rape a woman is a trait that evolved in men and was passed on from generation to generation because rapists would have outcompeted the gentlemen by siring more children. If it's really an adaptation, no man can really be held accountable for sexually assaulting someone... it's just "in our nature." 

There's a lot wrong about this, but I'll focus on two of the largest logical pitfalls. (For an excellent (and scathing) review by the blog Skepchick that goes in more detail, click here.)

The fact that something exists does not automatically mean it was selected for. Accidentally shooting yourself in the foot with a gun does not have an adaptive story behind it, even though people do it all the time, everywhere. For a behavior to evolve by natural selection, it needs to be heritable, variable, and convey fitness benefits.

And finally, the rape hypothesis is not falsifiable. Simply put, it's non-scientific. How can you prove or disprove a claim about behaviors tens of thousands of years ago? You can claim that spitting helped clean our ancestors' mouths out, but how on Earth would you test that? The ability to disprove a hypothesis is one of the most important aspects of science. If you cannot disprove an idea, it is no more valid than any other story you want to make up.

For simpler misconceptions regarding evolution, click here and here for blog posts I wrote in the past. 

Photo credits:
Selfish Gene - Wikipedia
Fox - The Guardian

Monday, July 22, 2013

Video game metal: Last Chance to Reason - "Upload Complete"

Progressive metal has regularly recurring themes, among them alien invasions, space travel, the human condition, dystopia, and other science fiction-based alternate realities. But the band I'll be talking about in this blog post takes the alternate reality theme to a whole new level. Last Chance to Reason's second album, Level 2, takes place entirely inside a computer world where the protagonist is an artificial intelligence that learns of the "outside world" and tries to escape. The band teamed up with indie developer Tom Vine and pixel artist Francis Coulombe to actually release a demo for a Contra-like side-scrolling video game where you shoot your way through hordes of zombies in tandem with the songs on the album. It's phenomenally insane, awesome stuff.
[EDIT 9-3-13: Last Chance to Reason drummer Evan Sammons was kind enough to share his thoughts on the song and blog post! Check out what he wrote at the bottom of the page.]

The first song on the album is called "Upload Complete" and is one of my favorite progressive metal songs, with plenty of growled vocals, imaginative lyrics, and guitar and keyboard wizardry. I'll highlight some of the tastier drumming in the following paragraphs. I've included time stamps from the drums-only part of the drum cover I did (second video above) so it's easier to see what I'm talking about.

0:00 - 0:20
A primordial soup of computer code, a mire of binary 1's and 0's slowly turning. Frozen numbers and letters waiting for the rush of electricity to bring them to life.

0:21 - 0:54
A jolt of power sets the world in motion. I think the first part is 11/16 and the second is 16/16. 

0:55 - 1:10 (6:13 in drum cover)
This is one of my favorite examples of a polyrhythm. While the snare maintains 4/4 time, the ride and bass drum (and rest of the band) play 15/16. The result is that each measure, the bass drum inches closer to the snare hit. Before I explain the polyrhythm, here's a quick lesson on time signatures:

This is a simple beat in 4/4. The base drum marks the beginning of the measure and the snare marks the middle. The 'o' is hitting the ride cymbal, hi-hat, etc. (You also hit it when you hit the base or snare, but for simplicity I didn't include an 'o' there.)


This is 8/8. It's not longer than 4/4; the space between the notes in 4/4 is just filled with another hit on the ride or hi-hat. It's the difference between counting "1, 2, 3, 4" and "1-and-2-and-3-and-4-and..." To play 7/8, just delete the 8th column in the figure (or don't say the last 'and' if you're counting aloud). 

Here are four measures of 15/16. Each  measure is two rows in the diagram. As you can see, the measure doesn't last a full 16 counts and instead appears to shift backwards. However, it only looks like it's shifting backwards because our reference is 16/16 here. When you listen to 15/16, you notice that it doesn't last the full 16/16 and the next riff starts 1/16 early, but after that it sounds normal. 

What's fascinating about 0:55 in "Upload Complete" is that the drummer Evan shows how weird 15/16 can sound by keeping that 16/16 reference. In other words, he keeps 16/16 (or, more accurately: 4/4) with the snare while letting the rest of the drums play 15/16. The result is a dissociation between his snare and the rest of the drums, making it sound like the two are drifting apart. In the figure below, the snare is maintaining 4/4 by always playing on the 5th note out of 8. The 'drifting' feeling can be seen with how more and more ride cymbal notes are between the base and the snare, and meanwhile there's the 'creeping' feeling of the base drum getting closer and closer to the snare. When they merge, the band ends this cool section and moves onward.

If you're still sitting there scratching your head, the drummer Evan explains it in this tutorial video. For the guitarists, here's a video explaining what the guitars are doing

The shifting drums also creates a really cool effect with the keyboards, which alternate between accenting the downbeat vs. the upbeat depending on where in the riff the drums are. The vocals sound sterile, inhuman, green letters sliding through the black space of the command prompt. This is one of my favorite progressive metal riffs... the beginning of an album as the protagonist enters the computer realm, the soft clean vocals in the midst of heavily-distorted guitars in the background, all representing the eye of the storm before the scream at 1:11, a blunt return to grim reality. 

1:11 - 1:47
Back to the world of shifting lines of code. The lyrics here are:

Pixels form to violent limbs
I am born, the end begins
I stumble,
physics format to this operating system

1:48 - 2:08 (7:07 drums-only)
This type of riff, where the bass drums are doing a constant roll and the guitars follow every note, is a classic progressive metal riff (here are examples from Between the Buried and Me and Protest the Hero). The structure makes it really easy to add or remove notes, as exemplified here with the alternating 9/16 and 11/16. This section is a great way to develop the song, an unfurling, steps carrying us into a new element of the story. It also transitions perfectly into 1:56, which introduces elements of grandeur. The huge undead cyborg coming over the horizon in the picture above from the video game definitely fits this part well.

2:09 - 2:31
A pause, catching your breath. I love the "erase or you will be erased," a fitting alteration of 'kill or be killed.'

2:32 - 2:43 (7:52 drums-only) 
Stumbling, trying to move forward but continually being pushed backward, upside down, losing all sense of direction in a storm. The vocalist Mike is growling "Critical: file transfer required" here, and I envision the protagonist encountering a tremendous divide that can only be crossed by attaching to a portal that disassociates you into your  fundamental binary code. If we're going full nerd, you can envision the divide as a membrane transfer protein or a catabolic cellular process that breaks you down, and you can only hope you'll be put back together on the other side.

2:44 - 3:00
Orbs of light scan my surface like curious children

3:01 - 3:15
While recording the drum cover for this song, at this point I noticed my left drumstick felt weird... whenever I hit the snare, the stick reverberated instead of feeling solid. There was a long cut going down half the stick but I kept playing, hoping I'd make it through the song before it broke. Nope. With no other sticks in easy reach (which would be a nightmare while playing live), I decided to try playing the rest of the song with half a stick. In the picture on the right, you can see half the stick dangling from the half I'm holding when it broke. 

3:16 - 4:07
This line is missing from lyric websites I've checked, but I think it goes:
As this update activates,
my limbs grow
with its effect on me

Followed by:
Erase or be erased

The transition to the next riff at 4:05 is pretty well-done. Here we've got two competing ideas for the drums: a fill to mark the end of one section and the beginning of another, and accenting what the rest of the band is doing. Why not do both? The drummer Evan follows the military march-style rigid guitars on the snare while sneaking in hits on the toms. I'd link to the part of the drum cover where I play this, but I never quite got it (read: totally messed that part up) so let's just move on, shall we? 

Another awesome example of the drums doing two things at once is in "Telos" by Between the Buried and Me. At the beginning, the drummer Blake is also doing a military-style snare riff and accenting the guitars. In the second part (once the vocals come in), he switches to maintaining the military riff on the bass drums with his feet, freeing up his hands to create a beat and push the song forward. 

4:08 - 5:32 (9:28 in drums-only)
The bass drums at the first part (and the end of the previous section before the fill) follow a triplet galloping pattern, a R-L-R-R-L-R-R-L-R with the feet. The system update initiates, waves of changes cascading around the protagonist. As the guitar solo begins, the drums expand upon a part of the fill from before the chorus, which works surprisingly well as a normal riff. One thing I definitely appreciate about progressive metal is that even without vocals, the guitars and drums can still an interesting story, albeit abstractly. Throughout the solo, the guitars range from a gurgling stream growing in intensity, wind whistling across a canyon, tanks crushing cars as they drive through a city, royal grandeur, the almost comedic madness of a swarm of bees, footsteps of a Terminator bursting into a run, and the final static-tinged silence of the aftermath. 

If you liked what you heard, here's a song off their upcoming album Level 3.

All images taken from the "Upload Complete" music video belong to Prosthetic Records.
UPDATE 9-3-13:
Drummer Evan Sammons comments: "It's amazing to see so much thought put into interpreting this tune! Not only did you get deep with the musical theory aspect, but you did a great job describing the visuals the music evoked for you. Tons of your interpretation of the story is right on with ideas we were trying to communicate. Even cooler is the fact that we wrote this tune so long ago that reading your exposition reminds me of things I forgot about the song. My favorite bits are where you have ideas about the tune that are unique and new to me as well. Your interpretation the "Critical: File transfer required" lyric is beyond what we envisioned, especially as you go full-on Ray Kurzweil in describing a kind of singularity, or consciousness upload. I dig it and it totally fits with the whole idea of the album. Thanks for all the kind words and sharing your ideas. Keep slaying those drums!

Wednesday, June 26, 2013

Competition avoidance drives foraging plasticity

A friend of mine recently published a great article that features several interesting topics in animal behavior research right now. The lab I worked in as an undergrad works on personality of threespine stickleback fish. Dr. Kate Laskowski, who just successfully defended her thesis last week, conducted an experiment that tested models predicting that a variable environment can drive between-individual differences in the plasticity of behavior. It’s a bit complicated but the implications are really, really cool. This blog post will be about how avoiding competition can drive different personality types. Dr. Laskowski was kind enough to provide a commentary at the end of the post. If you have access to an academic database, you can download the full article here.

Article details
- Laskowski KL, Bell AM. 2013. Competition avoidance drives individual differences in response to a changing food resource in sticklebacks. Ecology Letters. 16: 746-753.
- School of Integrative Biology, University of Illinois at Urbana-Champaign

Very brief summary
Behavioral plasticity is the ability to change your behavior in response to a change in the environment. Models predict that trying to avoid competition in a heterogeneous environment can promote between-individual variation in plasticity. In other words, if competition avoidance is possible, it'll be beneficial for individuals to consistently differ from one another in how responsive they are to changes in the environment (i.e. some are very responsive, others not responsive, and others in between). This study provides empirical support for these models.


- behavioral plasticity – the ability to change one's behavior in response to the environment. There is a cost associated with behavioral plasticity, for example the time spent traveling to a different foraging patch.

- between-individual variation – in a group, the variation between all the individuals. So,
how much one individual will differ from another individual. An increase in between-individual behavioral variation means individuals are behaving more consistently (decrease in within-individual variation) or there is a bigger variation in how the whole group acts.

In the graph on the right, you can see that by decreasing the within-individual variation (smaller bars) would increase the between-individual variation. Decreasing within-individual variation would mean the animals are behaving more consistently. (Note: in reality, this would be much harder to show as a graphic because you'd have lots of individuals, with many of the bars overlapping. This is an extremely simplified version.)  

- heterogeneous – non-uniform, patch. e.g. a salad is a heterogeneous mixture. (Contrast with homogeneous.)

- personality – more accurately referred to as “consistent individual differences in behavior.” These consistencies extend over time and across contexts. Personality has been documented in a wide range of taxa, from insects to primates.

- within-individual variation - how much one individual varies. As you take multiple measurements of a behavior, you will have variation because the animal doesn't act exactly the same every time. 

Article summary

Models on plasticity
In nature, we'd expect animals to be able to react perfectly to their environment (i.e. be perfectly plastic). Animal personality means that animals are not perfectly plastic, however. Animals don't conform to the best behavior for every context, instead differing from one another in aggressiveness, sociability, exploratory behavior, boldness/shyness, and more. This means the most aggressive fish in a group will still be the most aggressive across different contexts, like foraging, exploring, but also in the presence of a predator. The graph on the right, a reaction norm, illustrates this. Each line is a different individual.

Darwin's theory of natural selection clearly shows how variety can be beneficial. A species where everyone is identical means that the possibility exists that one flaw they all possess - susceptibility to a certain disease, for example - could wipe everyone out. Done, extinct, left only to artist's impressions in textbooks. But being different from one another in the case of personality isn't always beneficial; in an extreme example, some female fishing spiders are born so aggressive that they will kill any males before they can mate, meaning their genes never get passed on. (There's a lot of discussion on why limited plasticity should exist at all.)

Interestingly, not only are animals not perfectly plastic; they also differ in how plastic they are. In other words, individuals vary in how much they'll adjust their behavior to a change in the environment. Consider this example: a heavy rain leaves puddles of water in a forest that attract mosquitoes and other insects that lay eggs in water. According to currently-accepted behavioral plasticity models, some bats will shift their flying pattern to include these new sources of food, while other bats will stick to the spots where they've found food before. Think of it like deciding whether or not to eat at McDonald's or some new restaurant that opened somewhere a few streets over.

But now, picture that both McDonald's and the new place (let's call it Joe's) are severely limited in food supply. McDonald's only has 100 happy meals and Joe's only has 100 Joe burgers. You and 199 of your classmates have half an hour to eat lunch. Everyone used to just go to McDonald's without thinking about it, but now what do you choose? There's not enough happy meals, but who knows what a "Joe burger" even is? You're not sure where Joe's actually is, either. 

Some animal behavior models predict that this uncertainty about the environment can drive differences in plasticity. So while McDonald's was always open before (i.e. a stable environment), the appearance of a new restaurant (a change in food availability and distribution) could drive these differences between people's decisions on what you do on your lunch break (plasticity). To add an additional layer of complexity, social dynamics (who's in a group with you) have been predicted to also affect behavioral plasticity, but it's unsure how. It's like quantifying the effect of who's in the car with you when you're deciding where to eat.

Testing the models
As logical as these models (and the McDonald's example) may sound, there have been few studies on real animals to back up what the models say. Laskowski decided to test these models using threespine sticklebacks (right). Threespines are social fish commonly used in animal personality research, ideal for a study on behavioral plasticity and social dynamics. They're also easy to work with in a lab. 

Specifically, Laskowski tested these predictions:

1. When it's possible to avoid competition in a social group, the between-individual variation in plasticity will increase
 - Put simply: If everyone has the same level of responsiveness to the environment (e.g. a new foraging patch appears so everyone goes there instead of staying at the old patch), everyone will be competing for food. If it's possible to avoid this competition (e.g. the old patch is still there, so there's food for those who stay and those who leave will find food at the new patch too), there will be an increase in how responsive individuals are to a change in food availability.

 - If this is true, this should happen
When a new patch becomes available (and the old one remains), some individuals will consistently choose to stay and others will consistently choose to go to the other patch. (This differs slightly from the concept of ideal free distribution in that the individuals themselves will consistently make the same choice about staying or going, as opposed to just choosing where to go based on how many individuals are at each patch.)

- If this is not true, this should happen:
When a new patch becomes available (and the old one remains), individuals will just conform to ideal free distribution. Whether they choose to stay or change patches will be random and solely based on how many individuals are at each patch.

2. The social environment influences the variation in plasticity  
 - Put simply: Those around you can influence whether you consistently stay or switch to a different patch.

- If this is true, this should happen:
When a new patch becomes available (and the old one remains), an individual's tendency to stay or switch patches will depend on who is in the social group.

- If this is not true, this should happen:
The social group will not affect tendency to stay or switch.

Laskowski used two "regimes" to measure behavioral plasticity. In the "simultaneous patch regime," bloodworms were mechanically dropped into one side of a tank with six sticklebacks. After 5 min, half of the food was dropped into one side of the tank and the other half was dropped into the other side for 5 min. In the "sequential patch regime," after 5 min of food dropping into one side of the tank, the food started dropping into only the other side of the tank for 5 min.

Laskowski used six groups of six sticklebacks that were assigned to one of the two regimes. Each group was tested in two trials per day on five consecutive days to get the repeatability of behavior. The main variable she was interested in was switch delay, or latency to switch to the new patch.

To test the influence of social group, she then shuffled individuals between groups so that only two individuals from the same group were in their new one. Then, the fish were tested in the same regime as their original group. She also tested whether individual behavior in a group was related to individual behavior while alone. This was done by also testing fish from the simultaneous patch regime while alone. 

Data analysis 
Question 1: Competition avoidance
Bayesian statistics was used (as opposed to frequentist) with Markov Chain Monte Carlo simulations. Because there were multiple data for each individual - making the data  non-independent - Group and Individual (nested within Group) were included as random effects in the models. The repeatability of latency to switch patches, this experiment's measure of behavioral plasticity, was estimated.

Question 2: Effect of social group
A separate bivariate mixed model was used to estimate the covariance between switch delay in the original and shuffled groups.

Result 1: The opportunity to avoid competition promotes between-individual variation in plasticity
Individuals in the simultaneous patch regime showed consistent individual differences in switch delay (repeatability = 0.18, 95% CI: 0.05, 0.38). Individuals in the sequential patch regime showed very low between-individual variation (repeatability = 0, 95% CI: 3.0 x 10^-10, 6.6 x 10^-9).

This means that in the simultaneous patch regime, which allows for variation in staying or switching foraging patches, individuals did adopt a consistent strategy to avoid competing with one another. When there was no option to change your strategy to avoid competition (i.e. the sequential patch regime), there was no point in trying to act differently than everyone else. This makes sense, because there's only one source of food.

Importantly, the repeatability in the simultaneous patch regime increased over the course of the five days of the experiment. Specifically, the within-individual consistency grew higher. This means that individuals were becoming more consistent in their strategy. This positive feedback was not observed in the sequential patch regime.  

Result 2: Individuals maintain behavioral plasticity across different social environments in the simultaneous patch regime
In the simultaneous patch regime, there was significant covariance between an individual's switch delay in the original and shuffled groups. This indicates that in an environment where competition can be avoided, the social group does not influence behavioral plasticity.

In the sequential patch regime, there was essentially zero variation in switch delay between the original and shuffled groups, making it impossible to estimate covariance. However, this also supports that there's little carryover across social contexts. This means that for behavioral plasticity in patch choice, this study found no support for social environment having an influence.

Recent models have predicted that individual differences in plasticity are more likely to emerge in a spatiotemporally variable environment and when opportunities to forage are limited by competitors. This study provides strong empirical support for these models. Consistent individual differences were only apparent in the simultaneous patch regime, where competition avoidance was possible. This suggests that ecological factors such as food availability and predictability might influence variation in plasticity. Also, social environment did not have a strong influence on plasticity of switch delay: while individuals differed somewhat in their behavior between the two social groups (i.e. the covariance was not perfect), there was still evidence of consistency in behavior across the two groups.

This study also showed that the presence of highly plastic individuals in a population is likely to drive ideal free distribution, as competition decreases when plastic individuals hurry to the new patch and non-plastic individuals stay at the old patch. 

If you have access to an academic database, you can download the full article here.

The author comments - Kate's thoughts: 
"Running this experiment was a serious labor of love. Just collecting the data took a long time: I had so many groups of fish and they needed to be tested twice a day for five days. At the time, I only had one feeding arena in which to test the fish, so this mean that I could only test one group a week – resulting in a total of 15 weeks of data collection! I started having dreams about dropping bloodworms into fish tanks; it seriously felt like it was never going to end. But the really hard part of the experiment came with the data analysis.  I had to learn how to use R to run the Bayesian analyses, both of which I was completely unfamiliar with. Those were long dark weeks that I don’t remember a lot about other than staring at a computer screen for hours. But finally, I figured it out and was able to apply these fancy new statistical techniques to my data, which really improved the paper. And not to mention now, I’ve gotten quite good at both R and mixed modeling techniques which is an awesome (and very marketable) skill to have. So even though it felt like it took forever, in the long run it's totally worth it."