Flocking Science

Check out the beautiful video below of a “murmuration” (flock) of starlings acting in hypnotic unison:

Now, if you spend all day thinking about how to model biological systems (who doesn’t?), you might see that video and wonder about the rules each bird must follow to allow such spectacular emergent dynamics. Every individual bird probably gets some simple cues (direction, speed) from its neighbors, who get some from their neighbors (and that first bird), etc etc, and when these simple cues are acted upon and combined together all the birds form a giant complex morphing swarm.

A quick search reveals that the starling dynamics, and swarming behavior in general, have been the focus of a considerable amount of research and modeling. I’ll link this PLoS ONE paper since it’s open access (meaning everyone can view it in its entirety for free) and has some really cool videos showing off the modeling endeavors of the authors. In their simulation, each individual is characterized by parameters like mass, speed, position, and orientation- and these parameters get updated based on interactions with other individuals within a certain neighborhood. Just like in real life, these simple interactions scale up to show a swarm of individuals that behave as a complex, yet unified, group. (check out the videos in the link!)

I’ll also share this PLoS Computational Biology paper (also open access) which explores why individual starlings pay attention and respond to exactly seven of their neighbors (the authors report the number is special because it optimizes the balance between group cohesiveness and individual effort).

Another side effect of thinking about biology all day is always having to ask “Why (and how) did this evolve?” That is, what benefit does this intricate dance give the birds that allowed it to selected for and maintained? Being relatively ignorant of birds and their behaviors, it seems that such a show would turn into a buffet for predators. Well, maybe not. Here is a video of a Peregrine Falcon trying to snatch a starling during the flocking behavior and continually coming up empty handed (clawed?). The Peregrine Falcon is the fastest member of the animal kingdom, reaching diving speeds of over 200mph, so maybe this dizzying behavior is a great way to confuse even the quickest of predators.

I’m sure there is more to it than just predator avoidance, so feel free to add your 2 cents below!

Cool weather

The recent cold snap across the U.S. dusted off some neurons that hadn’t been used since Earth Science- and in the process I made a pretty cool (lol) connection with some images of Saturn recently released from NASA. The Earth has a vortex of cold air spinning around its North Pole, and in early January this vortex branched out and dropped a blanket of cold air onto the Americas.

Image Image

As you can tell from the above images, our polar vortex isn’t especially consistent or symmetrical in shape. The same can not be said for Saturn’s polar vortex


Credit: NASA/JPL-Caltech/SSI/Hampton University

The beautiful series of images above was taken from the Cassini spacecraft. “The hexagon”, as it’s known, has a hurricane at its center with cloud speeds of 330 miles per hour.


Credit: NASA/JPL-Caltech/SSI

It’s awesome to see well-documented phenomena on Earth taken to their extreme on foreign planets. Hopefully we’ll see more as we continue to explore the worlds in our solar system and beyond.

Check out more stunning images of the hexagon here.

Fun Fact Experiment

I tried something new with my Intro Bio lab students this semester. Every week I would have a new “Fun science fact of the week”- something relatively contemporary that I found exciting and had a (sometimes admittedly weak) connection to the current lab. I remember when I took intro bio lab things could feel a little stale and cookie-cutter, so I incorporated this as a way to spice things up.

For example- The week Voyager 1 left our solar system we were dissecting fetal pigs. I used this as an opportunity to show the slides of human anatomy stored on the Voyager 1 and describe just how similar pigs and humans are on the inside. This turned into a really fun discussion about space travel and genetic engineering. When we were discussing photosynthesis I went into some fun properties of light and the speed of light… which turned into a discussion about relative velocity and time dilation

When we discussed niche space I brought up the Radiotrophic Fungi discovered in Chernobyl. We then started discussing evolution and the “speed” of evolution. See, the fun facts naturally transitioned into a back-and-forth discussion among the students and myself. This set the pace and mood for the lab, and what might have been a stale lecture started off on the right foot as a passionate discussion about something fun.

The original plan on my end was that I would also blog about these facts every week and share them here… but it turns out grad school is pretty darn time consuming and my time allocation skills need refinement. There is always next semester!

Well, the results are in. According to my teaching evaluations the fun facts of the week were a big hit! Students looked forward to what the fact would be every week and share them with their friends after lab. In fact, after a few weeks I even had students emailing me with facts (“Hey, did you see this cool science video? Did you hear about this new research?” etc.) So, I would say the fun fact experiment was a success- and not just from the student’s perspective. I would get excited to see students excited about the fun facts, and looking forward to teaching every week certainly made preparations and grading less of a hassle!


More fun facts on here soon, I promise.


Cuban Treefrog (Osteopilus septentrionalis)


I am pretty sure this is a Cuban Treefrog, although please tell me if I’m wrong!


I let it go outside (sorry native frogs :-/). Anyway, it was definitely a neat surprise to find inside! That is, if you aren’t native to Florida yourself.


Carolina Wolf Spider

Carolina Wolf Spider

Hogna carolinensis, found in my apartment, Gainesville, FL.

The Second Most Astounding Fact

“The Universe is within us”

Alright, I can’t compete with Neil deGrasse Tyson’s fact for #1. But, I do know the second most astounding fact. There is a biological universe within us. Well, more like an ecosystem. A planet. Where interplanetary travel and colonization are possible. I’ll explain.

Lets consider “you” the planet. And by “you” I mean the ~30 trillion cells that you are comprised of that have “your” DNA- the cells that make you “you.” Now, your planet has many inhabitants that aren’t “you.” Entire communities that have colonized different parts of your body and work in harmony (synthesizing vitamins, aiding in digestion, etc.) with the planet they live in. In fact, at any given time, your body has about 10 times more foreign bacterial cells within it than its own cells (bacterial cells are much smaller than your own cells)***. And, on top of this, there is another order of magnitude of viruses that inhabit us (or our bacterial flora) for every bacterium.

***[Update: Other research suggests the number of bacterial cells within our bodies may be of the same order as our cells.]

Sometimes alien species invade our planet and (if our own immune system defenses aren’t fighting well enough) we combat them with antibiotics. However, antibiotics don’t discriminate against friendly and unfriendly bacteria, and can annihilate our friendly gut bacteria– leading to digestion issues, or even the recolonization of the gut with unfriendly species. (I’ll save fecal transplants for another post). One instance of this recolonization that has been receiving some press time recently has been of a homebrewer who had a population of Saccharomyces cerevisiae call his gut home. This single celled fungus, also known as “brewers yeast”, plagued the man by, well, doing what it does normally- metabolizing carbohydrates and producing ethanol as a waste-product. Not surprisingly, the condition is known as Auto-brewery syndrome.

Anyway, I always thought the existence of a microbiome within all of us was a really cool and astounding fact. At every instant of your life, there are hundreds of trillions of individuals living their lives within you. Awesome.

Our message to the cosmos.

In 1977 we flung an atomic powered robot into space. Voyager 1’s primary mission was to beam data back to Earth as it cruised through the outer solar system. One of the most famous bits of data sent back is this image of Earth captured as Voyager looked back towards its home planet in 1990 (Awesome commentary on this image and our planet/species by Carl Sagan here)


The Pale Blue Dot image taken 6 billion km from Earth in 1990.


Voyager, continuing with the momentum gained from its primary mission, has recently left our solar system and started its secondary mission of being a message in a bottle from our species to the cosmos. The message is stored on an easy-to-read golden record, and contains greetings in different languages, sounds from Earth, brainwaves of a human, and images from around the planet.


The Golden Record.

The cover of the record contains an easy to read explanation on how to retrieve the data– defining time units in the universal constant of the fundamental transition of the hydrogen atom. The location of our solar system is also printed on the cover, in relation to 14 pulsars with unique periods.

Check out President Jimmy Carter’s message to who/whatever finds Voyager- “This is a present from a small distant world, a token of our sounds, our science, our images, our music, our thoughts, and our feelings. We are attempting to survive our time so we may live into yours. We hope someday, having solved the problems we face, to join a community of galactic civilizations. This record represents our hope and our determination, and our good will in a vast and awesome universe.”

It’s awesome to know that there is a time capsule of our species and planet floating through interstellar space- likely to last billions of years in the cold reaches between the stars. I’d like the think that one day something pics it up and gets to hear Johnny B. Goode by Chuck Berry.


Successful Tracheostomy!

Well, successful in that they were able to inflate the lungs. I doubt the patient will do well post-op missing most of their other organs. This procedure was done by two of my students in tonight’s surgery lab. Also, check out the awesome stitch work by the students who removed a brain tumor!


On atoms and seconds.

There are more atoms of gold in your body than seconds that have passed since the beginning of the universe. (6.11 * 1017  vs. 4.354 * 1017 (that’s 611,000,000,000,000,000 vs. 435,400,000,000,000,000)). And what does this mean?

Well, nothing really.

I’m just trying to convey the awesome scale of the universe, both space and time, with some familiar terms. Warning: the links in the last sentence are pretty mind-blowing.

I’ll post soon on the scaling of space and time within the realm of biology, and how the space an organism takes up in space plays a role in the space an organism takes up in time (or, Lifetime vs. Body Size)

p.s. to calculate the atoms of gold from the wiki article: (2e-7 kg) * (1000 g / 1 kg) * (1 mol Au / 196.96 g) * (6.0223 atoms Au / mol Au)     (who said we would never need high school chemistry again?)

The Saddleback Caterpillar and Lepidoptera memory


I met this fellow in O’leno State Park  (along with a bunch of awesome Orb-weavers that I’ll probably post at some point). It’s a Saddleback Caterpillar (Acharia stimulea.) You can barely notice the ‘saddle’ on its back here, but I’m sure you have no problem noticing the venomous spines (known as Urticating hair) and mock-face (a startle display) on its backside. This larvae will eventually metamorphose into a limacodid moth:

Like many of the caterpillar –> butterfly/moth transformations, the adult bears little resemblance to the larvae in both body and behavior. It’s difficult to believe that the two life stages even belong to the same organism. In fact, what does the adult share with the larvae? Once in the cocoon does the body completely melt down and reform, leading to a rebirth and a fresh life? Or, does the adult have some memory of its youth?

Well, research suggests that the adults do share memories with their earlier selves. The scientists trained caterpillars to associate a specific odor with an electrical shock and found that, after metamorphosis, the adult moth avoided the odor that was associated with the shock earlier in life.

This shocking finding (sorry, I had to) may help scientists understand how Lepidoptera select habitat and, who knows, may have implications with human memory retention as well.