Tag Archives: biology

Awesome camouflage

Staying in the lab is tough when you live in the sunshine state. I mean, at SUNY Geneseo it was easier- the lab served as a warm refuge against those Western NY winds and clouds. So every once and again I’ll find a break in the Floridian sunshowers and bring my work outside. However, as any biologist can tell you, work is impossible outside because you always get distracted by some cool critter crawling by your laptop. Case in point: last time I tried this I noticed a little pile of moss moving across the table…


… so of course I flipped it over…


…and found legs! (Woah, I need to find out what this is.) Further investigation revealed impressive mandibles and a set of sticky spines:


It looked very similar to an antlion, which is the larval form of a certain family of lacewing. Antlions are awesome in their own right, they form little trenches in the sand and eat ants that fall into their trap. I teach an intro bio lab on the spatial distribution of organisms, and I always take the students outside to hunt for antlions (they are typically (spoiler) clumped together in sandy spots under the eaves of buildings). And I always show this video:

Anyway, it turns out that critter I found was also a larval lacewing! Certain species have sticky spines on their back that trap debris and help the larva blend in with their environment. This isn’t a new tactic- scientists have found a 110 million year old larval lacewing trapped in amber that has fern trichomes stuck on its back. How cool is that?! (Another spoiler: very)

And such is the curse of the biologist- go outside to write and in minutes you are a few Wikipedia pages deep classifying insects.


What’s in a species?

Take two biologists, sit them down, give them a few beers each, and then ask them to define the word “species”. Chances are you’re in for a colorful discussion. “Species” is one of those concepts that made perfect sense in high school, got fuzzy in college, and is something biology graduate students like to debate on the weekends.

Person A: It’s easy, right? If two organisms can create viable offspring, they are part of the same species.

Person B: Well, what about hybrids? You know, like when a horse and a donkey (clearly different species) mate and produce viable mules.

Person A: Well, mules are (usually) sterile, so that doesn’t count.

Person B: Ok, how about the viable and fertile offspring produced when Canids mate, like dogs and wolves or coyotes and wolves?

Person A: But those are recently diverged groups, I’d argue that they were actually subspecies of the same species (since they can produce viable fertile offspring, they’d be a subspecies by definition).

Person B: Alright Linnaeus, now you’re rewriting taxonomy. So you’re saying that as long as two organisms can produce fertile offspring, they’re members of the same species?

Person A: Right, but we can still define them into separate sub-species.

Person B: What about when organisms from two different genera produce viable offspring, like Fatshedera lizei ? 

Person A: Are the offspring fertile?

Person B: Well their are some reports that…

Person A: That’s a plant anyway, the rules are different for plants.

Person B: Wait, what are the rules for “species” in asexual organisms, especially when genetic code can be passed on by horizontal gene transfer? And what about cancer as a speciation event? You know, the idea that a tumor has a separate genome from its host so it should be thought of as a different species.

Person A: No way, man. Cancers are formed from and completely dependent on their host. It’s just an extension of a single organism.

Person B: Not necessarily! The Tasmanian Devil facial tumors are spread between hosts by contact. Why shouldn’t we consider those cells a unique pathogen, no different than a virus spread between hosts? And how should we classify that ‘organism’?

Person A: Are viruses even considered alive?

Person A+B: …I think I need another drink.

Yes, I’ve had similar conversations over the years as a biology graduate student. I was reminded of the species debate after reading about the “out of Africa” concept and human speciation, and whether or not we interbred with members of other hominid groups (and, what that means for the definition of our species).

Sleep with one eye open…

Who knew that the song Enter Sandman was actually about an interesting biological phenomenon? Turns out many aquatic and terrestrial mammals and birds actually sleep with one eye open! The corresponding hemisphere of the brain maintains wakefulness, while the other sleeps.

For instance, Mallards (pictured above) exhibit unihemispheric sleep as a way to keep an eye out for predators. Some aquatic mammals, such as cetaceans and manatees, keep one half of their brain awake to control surfacing for air while the other half sleeps.

The phenomenon of unihemispheric sleep has called into question the definition of sleep, its function, and whether it is even essential. Cool!

I stumbled upon the rabbit hole of unihemispheric sleep after watching this eerie video of sperm whales sleeping:

It appears that sperm whales undergo complete (bihemispheric?) sleep for 12 minute snaps, sleeping for just about 7% of their day, giving that whale the title of sleeping for the smallest percentage of their day out of any mammal (giraffes come in 2nd place with 8%).

This is why I love biology. Lets assume sleep is a biological necessity. Millions of years of evolution and adaptation has pulled this necessity in as many directions. From sleeping with half your brain at a time, or with the whole brain 7% to 80% of the day to everything in between. Biology is a healthy mix of ubiquitous phenomena and specialized solutions. Sometimes the hardest part is not clicking that one more wikipedia article all day.

1.1 Billion

That’s the number of heartbeats in every animal’s lifetime*. Don’t believe me?

Let’s consider an extreme comparison. A mouse can live for 3 years, and has a heartbeat of about 670 beats per minute. There are 525600 minutes in a year (365 days/year * 24 hours/day * 60 minutes/hour). So, that’s 3 years/lifetime *525600 minutes per year * 670 beats/minute ≈ 1.1 billion beats/lifetime. What about an elephant? They can live up to 70 years and have a heartbeat of about 30 beats/minute. 70 years/lifetime * 525600 minutes/year * 30 beats/minute ≈ 1.1 billion beats/lifetime. Woah… what?!

Ok, ok… you probably noticed that those “equals” signs are actually squiggly “approximately” signs, and if you did the math (you should!) you would see that they are both a little off from exactly 1.1 billion. But still, they are damn close. What gives? Why would the number of heartbeats be an invariant property of the animal kingdom? Let’s dive a little deeper.

The answer lies in allometric scaling, or how different properties of life scale with the body mass of organisms. It turns out that the power (energy per time, metabolism) required to support a given unit of mass of an organism scales with the mass of that organism to the (-1/4) power- meaning that smaller organisms use energy at a faster rate per unit mass than larger organisms. Other rates, such as breathing rate and heartbeat rate, also scale with bodymass^(-1/4). Lifespan, on the other hand, has been shown to scale with bodymass^(1/4). If you want to find how the lifetime total beats scale, you can multiply those two together (beats/time * time = beats). Bodymass^(-1/4) * Bodymass^(1/4) = Bodymass^0, which is always 1, meaning that the total beats is invariant of bodymass! More on allometry and metabolism in later posts. And maybe I’ll learn how to show equations in wordpress someday.

This paper (which probably takes into account more than the 2 points I used above) cites the total number of heartbeats in an animals lifetime as 1.5 billion.

Now, given this number, can we backtrack and use the relationship to see how long humans are predicted to live? Given a certain heart-rate, how long would it take us to use up our 1.5 billion?


R code:
curve(1.5e9/(x*525600), xlim=c(40,100), lwd=5,
ylab=”Lifetime (years)”, xlab=”beats/minute”);
abline(v=60, col=”red”);abline(v=70, col=”red”)

If an animal beats its heart between 60 and 70 times a minute, it would use up its 1.5 billion beats in around 40-45 years. Is this a ballpark estimate of a human’s lifetime in the wild? (Aside: if you take the 1.1 billion heart beats derived from mice and elephants and assume a heart-rate of 70 beats per minute for humans you get 29.9 years!)

Now, don’t worry. Humans have found amazing ways to increase their lifespan, and it’s not like everyone has a set number of heart beats to get through before it’s all over. This is just an interesting result of looking at metabolism and ecology – and what’s even more interesting is looking at the animals that stray from the predictions.

*That’s about the predicted number of heartbeats in an average organism’s lifetime

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!


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.