Tag Archives: science

Cone Snails: The reason why I won’t be sleeping tonight

TitleSometimes, when I’m camping, I dream about angry bears ripping through my tent and attacking me for that forgotten bit of food I left in my pack. A perfectly logical nightmare, all things considered, but far from my worst. In that one, I was SCUBA diving with my cat when she encountered a 6-inch long cone snail. In a sudden flash of activity, one of my best buds was murdered in a rush of sadness and a chorus of bubbly muffled screaming.

I must have been about 12 years old at the time I had the nightmare, and it keep recurring. These nightmares started the same night that I first learned about cone snails and their cat-murderingly lethal toxins from a Disvocery Channel documentary. Not once have I had a nightmare about a Badass Biology topic, let alone one that still rips at the psychological wounds 13 years later.

What about cone snails makes them so horrible? So memorable? Get comfortable, I have a lot to write.

The 6 reasons why cone snails deserve to invade my nightmares:

1) I’m convinced cone snails are heralds to the war of the end times.

Cone snails look pretty innocent. In fact, many of them, like the textile cone pictured below, have intricate colors and gorgeous patterns that would make them desirable for any unsuspecting shell-lover to snatch in an instant. Just look at this little guy here:

Textile cone. I’d would seriously be inclide to play with this shell if I saw it, then I’d remember this article and swim away in a panic. I’d likely also wet myself in fear. Image source: Wikimedia

How cute, right? I think so. I’d hold him. However, what I wouldn’t expect is for that fleeting joy to be one of the last thoughts my brain could process before I’d rapidly be dead.

Unlike the garden variety of snail, cone snails are carnivorous marine snails. They’re common in Indo-Pacific waters, though they also inhabit the temperate waters around California, the Mediterranean, and South Africa among other habitats. The smaller varieties eat benthic invertebrates, though the larger ones must be quick and deadly to capture the small fish they feed upon. This selection pressure created one of the most badass weapons in the natural world.

To catch their quick prey, cone snails possess a small harpoon-shaped structure within the snail’s radula, a feeding structure that other snails use to scrape food from surfaces. In cone snails, the harpoon carries a toxic cocktail of sometimes hundreds of lethal compounds, all stored in a venom sac that supplies the harpoon with enough venom to apply to their next murder victim. This harpoon is used blindingly quickly, leaving little chance for their prey to escape. Then, after that, the cone snails engulf them whole with a mouth so horrifying that I cannot find the guts to post a picture here, thereby I suggest you just Google it.


Pictured above is the anatomy of the venom sac and a microscopic view of the toxin-tipped harpoon. Image source: theconesnail.com

2) Take a moment today to call your mother and let you know you love her.

Cone snails produce more toxins than any genus of organisms discovered by science. In fact, there are so many that an entire database has been developed to catalogue and characterize conotoxins, the potent toxic compounds present in cone snail venom. This database, called ConoServer, presently has 8482 chemical entries from no more than 215 species within the cone snail genus, a staggering number for a single organismal group.

But what are these toxic chemical compounds? Most are peptides, short strings of amino acids chained together with a special carbon-nitrogen bond. If these chains were considerably longer, portions of the string would begin interacting with other parts and fold itself into a protein, a type of molecule I’m sure you’ve heard of. Peptides, though shorter, are still useful molecules to manufacture, forming the surfactants that keep mammalian lung tissue from sticking to itself, adding nutritional value to milk, and in the case of our nightmarish cone snails, killing stuff really really quickly.

Conotoxin peptides are mostly used defensively. Most human stings are caused by a wayward foot delivered to a cone snail hiding in the sediment. However, roughly 10% or so of classified cone snail toxins have been found to be used in foraging and hunting, paralyzing their prey.

3) I am now hoarding Morton’s salt under my pillow in case one tries to break into my home.

All of the 600-700 species of cone snails are capable to stinging and injecting their toxins into humans. Not only are there a multitude of lethal toxins in a cone snail’s sting, but their lethality is nearly unparalleled. A useful way to measure how lethal a toxin can be is to measure what’s called a LD50, or the dosage expressed in mass/kg of body weight at which 50% of a population of test animals (usually rats) are killed. Arsenic, a well-known toxic substance, has an LD50 of around 15mg/kg, meaning it would take about half a teaspoon of crystallized arsenic compounds to kill a male human weighing 83.6kg, or around 181 lbs. The LD50 for some conotoxins can be as low as 0.005mg/kg, meaning you could very well be killed by conotoxin at a volume little larger than 10 medium grains of sand.

How do these toxins kill at such small dosages? If you’re an avid reader of mine, you may remember textrodotoxin, a neurotoxin in blowfish that kills by interfering with ion channels in neurons. Ion channels allow neurons to fire, and conotoxins bind to these channels with startling specificity, prohibiting their ability to function. Conotoxins kill humans in much the same way, and like tetrodotoxin, most human deaths from conotoxins are related to the asphyxia caused by the diaphragm being unable to contract. There is no anti-venom, and in some species like the geography cone, a sting is 70% fatal.

4) I strongly suggest we flee for the mountaintops.

Diabetic or not, you’ve heard of insulin. Insulin too is a peptide, and in humans it acts a hormone to help mediate the amount of glucose present in the bloodstream. Cone snails have now added another use for insulin in the natural world.

In January of this year, researchers published a study characterizing two species of cone snails that possess the first and only recorded case of weaponized insulin in the history of the planet.

That’s right. Weaponized insulin. Used as a predatory tactic, cone snails release insulin into the surrounding water when prey are nearby. It then passes through the gills of prey fish, enters the bloodstream, and drops the blood sugar enough to prevent the fish from having enough energy to flee the encounter,  all in a matter of seconds.

5) Oh dear God, there’s more?!

Conotoxins are so potent that there are serious efforts dedicated to determine whether they can be weaponized and used on mass numbers of victims by terrorists groups. In a paper published in the Journal of Bioterrorism and Biodefense, scientists outline the probability of a terrorist attack in the form of aerosolized conotoxins or contamination of food or water. Their verdict is surprisingly reassuring, citing the difficulty to extract most conotoxins from living animals and the difficulties synthesizing conotoxins in a usable and deliverable form. However, not all varieties of conotoxins face these same issues, and the risk of three broad biochemical classifications of conotoxins are candidates for bioterrorism should those few key technical hurdles be overcome.

THIS IS WHY I KEEP HAVING THESE NIGHTMARES. GAAAAAHHH, DON’T SWALLOW MY CAT!!! Source: AquariumAdvice.com and my darkest nightmares

6) Oh hey, a fact that’s not actually all that terrible.

Remember when I mentioned ConoServer, the online database that combines efforts of dozens of biochemists seeking to catalogue the vast variety of Conotoxins? Why spend the time to catalogue them if terrorists could simply learn to replicate these peptides in vitro?

Many of today’s most common and effective pain-killers carry powerful negative consequences. For example, the narcotic pain medications like the opioids hydrocodone (Vicodin), morphine, oxycodone (Percoset), and codeine are highly addictive and can leave patients with withdrawal symptoms after their course is complete. The hunt is on for a powerful non-habit forming pain killers with few side effects that can be cheap, easy to deliver, and easy to scale up.

Conotoxins may provide the solution. Much like snake venom, most research efforts on conotoxins are geared toward repurposing the toxins to serve as pain killers. Perhaps a single toxin or a cocktail of a few or several toxins could serve as potent yet non-costly painkillers, and collaborative research efforts like ConoServer could rapidly speed progress towards a revolution in patient care and pain management.

One promising conotoxin pain drug is ziconitide, a synthetic drug identical to a toxin produced by the cone snail Conus magus. Ziconitide has been FDA-approved for treating intractable pain and has shown some promise in its effectiveness. However, the drug degrades rapidly and cannot be delivered orally. Instead, ziconitide must be injected directly to the spinal cord via a surgically-implanted pump. Not terribly convenient if you ask me, but it seems to be a good start nonetheless.

Progress is being made to develop oral conotoxins-derived pain medications. In 2014, Dr. David Craik from the University of Queensland presented new evidence at the 2014 meeting of the American Chemical Society. Craik and colleagues looped peptide chains, amplifying their stability over the long-term while preserving their potency as analgesics. The prototype drug was given orally to test animals and showed nearly a 100-fold increase in effectiveness in comparison to the common painkillers morphine and gabapentin.

Overall, I find it pretty badass that such an effective killer lurks in the oceans. It delivers death in seconds to its prey and in minutes to a fully-grown human, and with no anti-venom, its effects are second to none. Hell, these guys even weaponized insulin. On top of that, they may gift humanity with a revolution in pain management. That’s pretty badass.

Want to suggest a future topic? Write it down in the comments below. Do it. Do it do it do it doitdoitdoitdotidoit.

For further reading:

http://www.conoserver.org/?page=about_conotoxins&bpage=keyrefs (list of current review papers on conotoxins as pain killers and the difficulties faced with their use)

http://www.theconesnail.com/ (lab website of the Olivera lab group at the University of Utah)

Don Cowlione: How Cowbirds Run A Songbird Mafia


If I were to imprint on you one main point stringing together every article I’ve ever written for Badass Biology, I hope it would be this: nature has produced no shortage of jerks. I say “jerk” like it’s a bad thing, but take the time to think about the word and you’ll realize “jerk” becomes a bit endearing when we’re talking about nature.

First, let’s review what it means to be called a “jerk” species. First, a jerk has to be abundant enough to merit some sort of attention or recognition, but not more abundant than non-jerks, otherwise the jerk strategy would be much less effective. This population size balance is very delicate, but jerks seem to manage it well.  Second, being a jerk means going against some established natural norm. Usually, jerks exploit some mutually beneficial arrangement between individuals, leaving another party to carry their weight for them. It’s a pretty clever strategy if I say so myself. Third, present a jerk with an opportunity and it’s likely to get snagged. Another admirable trait in favor of biological jerks

Back to the point, Planet Earth has lots of jerks. Consider the bluestreak cleaner wrasse. On Southeast Asian reefs, cleaner wrasse set up cleaning stations where they pick off the tiny parasites that live in the skin of larger fish. This arrangement seems to work for everyone (except the parasites, unfortunately); the wrasse get dinner while the larger fish get a good skin treatment. Some jerk wrasses, let’s call them “wrasseholes”, like to instead bite big chunks out of the mucus membranes on these fish instead, turning this mutualistic interaction into a parasitic one.

To be honest, it’s not that I find this interaction all that neat. The main reason I bring this up is to mention that it DID spawn an article in Discover Magazine with a really clever name: Cheater Cheater Mucus Eater.

Sure, jerks are great and all. My favorite? This little guy:


Adorable, right? What about now?

The Birdfather

Why yes, I AM proud of this joke.

Make no mistake. This stone cold killa is ruthless, even enough so that I’d put the word “killa” in an article that I’m reasonably sure a future employer will read.

So what about this little bird makes it so much of a wrassehole? To start, an introduction. This is the brown-headed cowbird, a member of the family Icteridae, which consequently means nothing at all to me but sounds pretty badass all the same. What distinguishes cowbirds is that they are notorious brood parasites. They find nests belonging to other aviary families, mostly songbirds but varying from hummingbirds to birds of prey, lay their eggs next to theirs, and let those other poor bird parents feed, raise, protect, bathe, clothe, and attend PTA meetings of cowbird babies. As of 1999, approximately 140 species of birds have been documented raising cowbird young.

Here’s what’s odd about this. I’m sure you’ve guessed that cowbirds are able to get away with this sneaky business because their eggs and young look an awful lot like the birds they’re parasitizing. They don’t. More often than not, cowbird eggs are either much larger than the eggs of their host AND a different color and pattern. Moreover, cowbird chicks are gigantic when they hatch, making little songbird chicks look tiny by comparison.

One of these eggs is a parasitic cowbird’s. Can you guess which one? Did you guess the one on the bottom left? You did!? Very good!

You may be asking yourself, “why do these other birds raise babies that aren’t their own?” Right now, I’m asking myself, “have I smelled like this all day?”, but that’s really of no consequence to anyone (except my wife, I guess).

Oddly, one theory explaining why the hosts hadn’t murdered these little guys is, and I’m serious, that the host birds don’t have the cognitive ability to recognize that these chicks are different from the others. It seems odd to me that the same birds can relocate their nests among thousands of other similar-looking forest objects with near-identical colors and patterns would not be able to recognize that one of their babies is a freakish monster.

Meanwhile, I only learned today that I live 5 minutes from a major interstate highway, but I’m confident that there’s no gigantic monster baby living in my house. One of our cats is pretty large, sure, but I’m not convinced I’m her father or anything.

No, the real reason host don’t viciously murder cowbird young is pretty sinister. In 2007, two researchers from the University of Florida set up a field experiment where they manipulated cowbird presence in predator-free nests of host birds. In “ejector” nests, the researchers removed cowbird eggs from host nests, mimicking a host that rejected a cowbird egg,  whereas “acceptor” nests saw through the raising of a strange foreign cowbird hatchling. In all, 56% of ejector nests saw some the destruction of host bird eggs, but only 6% of acceptor nests were ruined. What happened?

Cowbirds happened. Females, actually. These jerks monitored the nests of their hosts, checking in on the progress of their young from time to time. If cowbirds found that their babies weren’t receiving the star treatment (or weren’t in the nest at all), the cowbirds would lay ruin to the eggs of the host bird. Essentially, these birds were exhibiting mafia behavior, laying down some pretty severe consequences if the host rejects the parasite.

What’s equally sinister is the explanation for destruction in the 6% of acceptor nests. Why kill the young of a nest that’s satisfactorily caring for your own young? Simple: murder creates room in the nest for more cowbirds.

In summation, I quite admire cowbirds. In a group of organisms whose ability to distinguish which egg is their own is questionable, these ladies are clever. It’s pretty rare to see such a sophisticated racket exist in animals with brains the size of beans. Think about the cognitive power cowbirds need to keep track of which nests are parasitized, then decide on whether to murder or not murder depending on what they see. I gotta say I’m impressed.

So, like a Don collecting tribute from his corner of Little Italy, cowbirds command respect. They’re clever, manipulative, aggressive, greedy, and all of it is so sinisterly bundled in a package that I’d rather enjoy petting.  Plus, it’s nice to know that some species out there gives others an offer they can’t refuse.

The 6 rules every grad student needs to know well

(EDIT: Contains minimal biology. Deal with it.)

The past 7 months have been the busiest and most stressful of my life. I decided to abandon my plan to become an academic to move back home and pursue an industry job, where, from an academic’s perspective, the ranks are filled with fat cats that do shady business via coordinated rubbing together of the hands  and menacing ear-to-ear grinning, and where even the low-level employee cubicles are lined with millions of ill-acquired dollars taken from the penniless hands of the National Science Foundation, National Institutes of Health, and [insert your favorite noble scientific organization here].

Before I could graduate and thrust my resume into the tens of thousands of already overflowing piles of identical resumes seeking to get the same entry-level industry jobs as I sought to acquire, I first had to do all of the following within 7 months: 1) design and complete the largest and most ambitious experiment of my research career, 2) author and defend a Masters thesis from scratch, 3) teach an undergraduate lecture course by myself, 4) help my busy fiancée plan and execute a wedding and honeymoon, and 5) coordinate a cross-country move, using only a 4-door Honda Accord to fit everything I own.

So, if you had any question what I was doing with my time over the past few article-less months, please read the above paragraph. Please try not to wince as hard after reading it the second time through.

How did I get all of these things done? Here are a few simple laws that helped me see through all of these goals at once:

1) The 80-20 rule:
Developed by 1906 by the Italian economist Vilfredo Pareto and recently popularized by Timothy Ferris in his stimulating bestseller “The Four-Hour Work Week”, the 80-20 rule describes that, in many situations, 80% of the effects come from 20% of the causes. In business, this might mean that 80% of your income comes from 20% of your clients, or that 80% of your losses come from 20% of your setbacks, and so on. In my case, 20% of my urgent tasks were causing 80% of my stress. This dynamic rule forced me to identify what tasks needed my attention the most and foresee what positive effects I might expect as a result, allowing me to prioritize where my efforts needed to be expended.

2) Don’t drop the same ball twice in a row:
Early in my grad school career, my PI sent an email to the entire lab with advice that read something like the following: “If you have to balance many important tasks in one day, such as work, family, research, and school, you may not have time or energy to adequately address all of them. It’s OK to let one of them go unnoticed. However, it’s whenever we fail to address the same thing several times in a row that the problems begin.” My alteration to the rule: don’t let the same task go unaddressed for two consecutive days. No task got rusty or completely left my mind if I devoted at least a little bit of time to it every other day.

3) Identify and minimize wasted time:
Like all of us, I get distracted by things that are more fun than work. How do you identify what’s the MOST distracting? Simple: RescueTime. RescueTime is a free application that creepily monitors your activity on your computer, categorizes your time by category, and highlights which applications are the most productive or distracting. For example, RescueTime knows whether I’m playing video games or surfing Reddit, and runs a clock to monitor how much time I’ve wasted on each activity. At the end of the day, it alerts me with a report on how much time was productive and builds a profile of my daily and weekly productivity. Your goal should be to beat your previous day’s (or week, etc) productivity score.

If the internet is your big time waster, try StayFocusd. This simple browser add-on allows you to input which websites (Reddit, YouTube, Facebook) rob you of the most time. You can then set a time to share between all sites on your list, and a counter will appear displaying your remaining time on those sites. For example, I allowed myself only 30 minutes per day of combined Reddit and Facebook time. After the 30 minutes, StayFocusd would block access to those sites on my computer, leaving me no way to access them once the clock has run out (unless I disabled the add-on, but that’s cheating).

4) Drink heavily and cry Prioritize sleep over poor-quality work:
Know and understand how sleep can enhance the quality of your workday without increasing the time you spend working. Each person has their own limits and needs; for the lucky few that are alert all day after 6 hours or fewer of sleep, I envy you. I need about 8 plus a 20-minute power nap around 4:30. Others need 10 or more. Experiment on your own, graphing your RescueTime productivity score (y-axis) as a result of the hours you slept the night before (x-axis). After a week or two, clear patterns should start to emerge, and you’ll find your sleepy sweet spot. Once you do, make that amount of sleep your priority, otherwise the quality of your work may decrease with increasing stress.

5) Break large tasks into small ones, each chunk with a firm deadline and a small reward:
Following this rule allowed me to write my graduate thesis draft almost without issue. First, I’d set aside an entire day per week for thesis writing, not worrying about research or teaching or any other day-to-day activities (but not for two consecutive days, see item 2) above). Before I began, I’d spend 5-10 minutes devising my goals for the day: take a section, break it into unambiguous chunks, assign a short deadline for each chunk (see below), and list the reward for finishing on time. Your rewards must be small, like a 10-minute cookie break or a brief play session with the dog. My favorite reward: use the remaining time until your deadline to do whatever time-killing you want to do. If you fail your deadline, you get no reward. Alter your deadlines if you miss them frequently, but it’s important to keep them short.

6) Assign absurdly short personal deadlines:
Another Ferris-popularized idea is a rather clever one; when you assign deadlines, make them shorter than you originally anticipated, within reason. Large tasks often take until the very end of the deadline to complete, so by shortening the deadline, you’re forced to work more diligently and more precisely without truly rushing. Say you’ve got a paper that’s due in 3 months. It will take you from now until the 3 month deadline to think, outline, write, edit, and review the paper, turning it in only at the very end (or at least near it). Instead, shorten that deadline to a single weekend, and you’ve now freed up so much time to devote to tasks that may be more important or urgent. I used this rule for my thesis; during a meeting, my PI asked for the first draft in 8 weeks. Instead, I suggested to make it 4 weeks, forcing me to live up to my goal while still having enough time to get good work done.

This is by no means a comprehensive list of constructive suggestions. These are just 6 things that I found were helpful towards preventing me from feeling overwhelmed.

Now that I have completed all of these really difficult tasks and am looking for full-time employment, I have more time to spend sharing science again. It’s a comforting yet horrifying thing, unemployment. On one hand, I have so much more time to devote to science communication, one of my truest and most rewarding passions. On the other, OH MY GOD IM UNEMPLOYED WHY DO I HAVE SO MUCH FREE TIME YET SO LITTLE MONEY.

In the end, I’m glad I made it through the past 7 months. I now have a Masters’ degree, a loving wife, and work experience that should make hiring managers scramble to send me their official job offers. I don’t mean to brag too much about my accomplishments. I’m just proud that I’ve seen my goals through and have made it to the other side. I wish you luck on doing the same.

Check back soon for more Badass Biology articles, and as always, comment if you have a badass science topic you’d like me to cover!

How palindromes allowed males to exist


If I were asked to give my two most valuable pieces of advice, they would be these: First, appreciate the near impossibility that you are alive. The atoms that make you have been through some shit; they’ve swirled as stardust, formed a hot molten planet (or crashed into one from elsewhere), boiled, compressed, and decayed to a point where they were incorporated into who-knows-what part of a who-knows-what number of a who-knows-what kind of strange prehistoric organism before they now make you, sitting comfortably at your computer marveling at my repeated usage of “who-knows-what”s. The other piece of advice? Never try to drink a beer without using your hands.

Without getting abundantly philosophical, you by all means shouldn’t exist. I ask that you, at least once daily, come to terms with this fact. Appreciate also that you can come to terms with anything at all, you big-brained multi-talented sculpture of evolution. Appreciate that other humans exist that can love you and carry out services to make you more comfortable. Appreciate pizza, because how did the universe create something so perfect?

Oh, and if you’re male, go ahead and appreciate that you exist. You theoretically should not.

In evolutionary terms, males are dispensable. The adaptive value of males is that they can mix up genes to create new combinations of traits on the off-chance that some of them can help prevent an untimely death, aid in making little ones, or allow one to be more comfortable overall. Males are gene donors. That’s basically it. Yeah, some males aid in parental care or perform tasks to aid group survival, but male uselessness is a common evolutionary motif. Male anglerfish are prime examples.

Gender in humans (along with a lot of other species) is determined by the identities of a pair of sex chromosomes contained in every cell. Both males and females possess one X chromosome, a large and gene-packed chromosome chock full of genetic goodies. Females have a pair of X chromosomes, one from the mother and one from the father. Males, however, have only one X chromosome, donated by the mother, and a shrimpy and scrawny Y chromosome donated from the father. X chromosomes contain some 2000 known genes, Y contains only 78. Bummer.

There’s a good reason why the Y chromosome is so scrawny: DNA damage is pretty common. Being so long and fragile, DNA can become knotted, coiled, unwrapped, kinked, looped, mutated, irradiated, copied wrong, fixed wrong, proofread wrong, chopped, sliced, chunked, choked, broken, inverted, doubled, misread, and misunderstood. Each of your cells possesses a SWAT team of enzymes that try to prevent these things from happening, but they’re not without error. Mistakes happen. So, because our cells possess 2 copies of each chromosome, when one becomes overly mangled, these enzymes can use the other as a template of instructions to repair the damage.

X chromosomes do this beautifully. These, in short, scan each X chromosome and check for inconsistencies, using one or the other to clear up any mismatches in DNA code. Two similar chromosomal regions can also “cross over”, exchanging segments of DNA that encode for roughly the same type of protein. Most of the time, crossing over is beneficial because it throws some genetic variety into the mix.

Crossing over is like holding hands, only after you’re done, your hands trade bodies. Good old nightmare fuel.

X and Y were once paired just as healthily as two X chromosomes are today: both were large, bountiful chromosomes that crossed over frequently and used each other as repair templates. About 300 million years ago, as reptiles and mammals diverged, a mutation caused the Y chromosome to take on more “manly” attributes, including the development of testes, sperm, different hormone production, etc. X and Y were now very different chromosomes. Crossing over ceased between them. Cellular machinery stopped using one to proofread the other. They became distinct and wary of the other. The X chromosome still had a healthy pair in females and could easily use one to keep the other functional, preserving the integrity of the chromosome.

Unfortunately, Y became a genetic desert island, left all by its lonesome with nothing to use as a spell checker in case things went very wrong with its code.

By this logic, many scientists think the Y chromosome should have been obliterated. With more and more DNA mutations accumulating, more and more of the chromosome was snipped away and discarded. To make matters worse, portions of the chromosome inverted themselves. Areas swapped information, mixing things up further. The Y chromosome was rapidly becoming giant mess. Eventually, removing all these errors caused Y to become tiny, almost biting the dust altogether and doing away with males entirely! But it’s still kicking even after 300 million years. With no partner to help proofread its DNA, how did the Y chromosome survive?

DNA and language share many things in common. Almost too many. One of them is that segments of information, called palindromes, can be read from left to right or right to left and read the same way: God, a red nugget, a fat egg under a dog! DNA contains palindromes too, and they can be long, sometimes hundreds of bases in length. The problem with DNA palindromes is that they are a liability; because bases like to chemically pair up with their counterparts, segments of independent DNA can stick together to form looped hairpins, derailing the important cellular machinery necessary for replicating, proofreading, and transcribing DNA into proteins.

Palindromes on two strands of DNA can join to form hairpin regions. These are bad. Imagine a train barreling down track shaped this way and you get the picture.

The Y chromosome in particular is full of palindromes. Normally, high palindrome density is a chromosomal death sentence. However, in the case of the Y chromosome, palindromes were a blessing. Because the Y chromosome had so much repeat information and no paired chromosome to proofread it, Y could use different segments of ITSELF to validate that the information on another segment was correct. Y chromosome palindromes kink together and use one strand to proofread the other, turning large segments of the chromosome into genetic hairpins. Because both are palindromes, one segment should read exactly the same as its folded-over counterpart. So, in a sense, the Y chromosome uses what’s normally a huge flaw as its primary means of keeping information correct.

As an added bonus, this method of palindrome proofreading can create new varieties in the DNA code akin to crossing over in X chromosomes. When one strand is damaged, the enzymes responsible for repairing it can’t distinguish the damaged strand from the undamaged one. All it can do is discriminate one from the other. Therefore, it has to guess which of the two sides needs fixing. Often, this can cause the undamaged segments of DNA to take on the information of the damaged counterpart, creating new combinations of DNA code to form. While this could possibly ruin the genetic meaning of the original, it also presents an opportunity for new traits to become expressed on the ever-changing Y chromosome.

Self-repairing Y chromosome palindromes at work. This is something I’ll surely bring up at the table come Thanksgiving.

I cannot over-emphasize how important palindromes are to the sustainability of the Y chromosome. Without this ingenious little method, human history would have played out very differently. So, while palindromes can be a fun way to parody a Bob Dylan tune, be thankful that they also keep you healthy and keep your identity in check. Add that to your list of things to appreciate.

A special thanks to Sam Kean, whose book “The Violinist’s Thumb” encouraged me to write this article. It’s a fantastic read, I highly suggest it.

For more information:



Alpine swifts’ 200-day non stop flight

Original photo credit: D. Occiato- http://www.pbase.com/dophoto

You know how damn exhausting it must be to fly? I don’t. Having never had the ability to fly without propulsion, I can’t say just exactly how hard it must be. Studying the metabolism of flying birds gives us some idea, and current evidence suggests flying is really really f**king hard.

A lot of people compare flying to swimming, which I think is a bit of a BS comparison. Water is a much more dense and heavy medium than air. Sure, it’s harder to move through water than it is to move through air, but long-distance travel through the oceans has the advantage of buoyancy to counteract the effects of gravity. Without having to spend energy from falling to the ocean bottom, all effort can be spent moving forward.

In contrast, flying truly is falling with style. Most of the forward energy generated from flight occurs because of gravity, or the downward force of the wing generating movement in the forward direction. Thus, flying animals are tasked with the mind-numbingly complex task of controlling their descent and forward travel, modifying body position as air currents change, all in an attempt to keep oneself from crashing into the ground in a puddle of crushing sadness.

Basically, it’s generally agreed that moving flying is more energetically demanding than swimming or walking. Migratory birds that choose to embark on long-distance flights typically rest for a while throughout the journey. Even the largest sea-faring gliders have to rest every few days to recover from their grueling haul.

Unless you’re the alpine swift. These aviary ass-kickers don’t stop for jack shit.

“But don’t birds have to land on the ground to eat, rest, or sleep?”. F**king nope, not the Alpine swift.

These birds are built for ass-kickery. They have a body design that’s conducive for long-distance travel, mixing flapping and gliding to travel long distances using little energy. And their yearly migration is a long one, beginning in the mountains of Western Europe across the Mediterranean and Sahara to their wintering sites in the African interior and back, a journey spanning some 2500 miles round-trip.

Migration routes and non-breeding range of three Alpine swifts breeding in Switzerland.

Migratory behavior of the three birds assessed in the study published by Leichti et al. Each bird is a different color, and the arrows represent periods of non-stop flight (Figure 1 in Leichti et al 2013, link below).

There have been rumors for decades that some swifts never land for any reason, which honestly sounds ridiculous and stupid. So, to resolve the stupidity, a group of Swiss researchers placed sensors on six Alpine swifts, seeking outline their migration from the Swiss Alps to western Africa for the winter. What they found, described in a paper published in the October 2013 issue of the journal Nature Communcations, ended up being so mind-blowingly balls out that I myself can hardly believe they didn’t just make it the f**k up.

The transmitters they used collected only two parameters: light level to extrapolate position, and acceleration to determine other metrics like pitch (a measure of body position, indicating whether the animal was in flight and where it was traveling), flapping rate, metabolic activity, and a few others. They were also able to tell when and where birds were breeding, wintering, or migrating based on how the birds behaved and where they were located.

This is the tiny transmitter used by the authors to collect data over an entire year. Science! Source: https://www.sciencenews.org/sites/default/files/images/js_tiny-data-logger_free.jpg

Based on the distinct difference in activity between roosting and migrating metabolic activity and pitch, the researchers observed that the three birds they recaptured in Switzerland the following year had been on the wing for at least 200 days. Every bit of food they ate over the trip was snagged in the air during migration. And sleep? Well, the authors aren’t really sure whether swifts feel the harmful effects of sleep deprivation:

“In Alpine swifts there seems to be no necessity for physical inactivity to maintain any of the relevant physiological processes. However, our data indicate that there are distinct periods of increased and decreased activity, which could go along with some kind of sleep in flight.”

Such periods of decreased activity suggest swifts spend several nighttime hours gliding to conserve energy or perform other physiological functions. The researchers’ data backs this up too; swifts were most active and had highest flapping rates near sunrise and sunset, probably because they need to ascent to great heights to avoid gliding into the ground overnight, and probably had to work to recover this altitude at sunrise. How do they control their flight if they’re asleep? Nobody really knows, but they may only sleep one brain hemisphere at a time.

So, despite hours of grueling physical activity, swifts seem to recover without having to land on the ground or water. They travel huge distances over impossibly barren terrain, hauling ass with more long-term gusto than any land creature ever documented. They’re masters of endurance and champions of travel with a purpose.  Also, never challenge one to a “lets’s see who can fly the longest” contest. Literally every other organism on the planet will lose.

Want to suggest a topic? Write it  in the comments below!

Further reading:








Humanity’s Most Badass Adaptation II: Sucks to be small

Why Ant-man is the worst superhero ever.
What if we were much smaller? Well, there’s good and bad news. The good news is that we could adopt simpler body forms, but that’s about it. The bad news? Pfft.

First. we would probably be much dumber than we are. Zoom in closely on the brain of every animal and you’ll find neurons, cells that communicate to one another using electrical or chemical signals. Hundreds to thousands of these neurons form dense and complicated circuits with one another in the vertebrate brain. Such circuits form pathways that tend to perform specific functions in the body. For instance, there are specific regions of the brain designated for movement, for regulating sleep, for hunger, for balance, for typing “guns and missiles”, and for interpreting the sights, sounds, and smells from the world. Our bodies may be able to shrink in size and still function to some degree, but our neurons cannot only be miniaturized and still function with such complex synchrony and elegance. As we grow significantly smaller, we run out of room for neurons very rapidly.

“But Kevin, I’ve always heard that a big head doesn’t mean make you smarter”. Don’t you sass me. But you are right, anonymous naysayer. There is admittedly weak evidence that intelligence correlates with head volume, yes, but that’s among humans of relatively the same size [3]. For example, my fiancée is tiny and adorable, though she’s likely smarter than I am (Fiancée et al, 2014). However, when we’re talking about a difference in scale between us and a mouse, size matters. We have nearly half the number of neurons as the U.S. military has guns and missiles, something around 86 billion neurons [5]. Mice have around 10 million. Ants have around 200,000. To put this into perspective, if each neuron were a person, our brains would outnumber earth’s human population 12 times over. A mouse’s would be constrained to the size of North Carolina. An ant’s would be Laredo, Texas. It’s hard to grow intellectually when you’re Laredo, Texas.

I apologize to anyone from or living in the city limits of Laredo. I did not mean to say your city is dumb. However, it certainly looks that way. I’ve visited your website. It looks terrible.

Come to Laredo and visit our…moon.

Being the size of an insect would present a number of other challenges. The interactions we have with things in our environment (like the water we drink and the food we eat) conform to the laws of physics. As we shrink in scale, these interactions change. To an ant, water seems as viscous as maple syrup. Gravity takes a backseat to air turbulence. As Steven Jay Gould writes, “An ant-sized man might don some clothing, but surface adhesion would preclude its removal. The lower limit of drop size would make showering impossible; each drop would hit with the force of a large boulder. If our homunculus managed to get wet and tried to dry off with a towel, he would be stuck to it for life. He could pour no liquid, light no fire…” [2].

Could an ant-sized version of early man have developed civilization even if intelligence were not a factor? Probably not, at least not at the same rate or with the same level of success. I imagine cultivating agricultural crops, one of the supposed precursors for civilization, would have been near impossible, not to mention cross-breeding them for good yield. Our meat-based diet would be replaced with who knows what, but I suppose it would include plant material and any nearby organism that decides to die. For that matter, hunting would be folly; spears and bows would be completely ineffective because we probably couldn’t put enough force behind the blow. Guns and missiles wouldn’t exist. Our predators would vastly rise in number, distancing us from the top of the food web. We’d be stomped into submission by the elements, by other creatures, and by our own ineffectiveness. Switzerland would be near impossible to get to. So long, Mürren.

What about food? Shouldn’t food be more abundant since, you know, one kernel of corn could feed an entire village of people? That’s true, but there’s a much bigger caveat to this than you’d think. The world’s food is spatially patchy. I don’t just mean that bananas only grow in the tropics or that rice grows best in silty soil. I mean that, when you’re the size of an ant, getting a bug from the ground nearby is a marathon. Food sources are really f**king far apart, but plentiful once they’re found. Many animals that live upon such food sources adopt life strategies to cope with smorgasbord-style resources. Some insects that exploit huge but infrequent foods, including flies like the gall midge, have adaptations that allow them to exploit them quickly. Gall midges typically reproduce sexually, though it takes a long time for larvae to develop this way. When midges find a mushroom, a gold mine on their scale, females reproduce without a male through a process called parthenogenesis. These offspring are formed more quickly than doing things via the sexual route, though it comes at a cost to the mother. Instead of developing externally, the larvae grow inside the mother, eventually liquefying her insides and bursting from her lifeless husk [4]. However, immature as they may be, they are ready to start chomping away on some sweet sweet mushroom bits and rotting parts of their mommah. D’awww. Overall, the flies have more successful babies this way, thus the need for bursting out of their moms and such.

Will humans do that? I dunno. That sounds desperate. But food would likely be lacking for most humans on earth. Maybe we’d be as successful as ants and develop complex chemical signals to communicate the locations of food, bypassing any other weird adaptations like the ones midges have . Maybe we wouldn’t, and we’d fill just another tiny niche in the complex world which we inhabit.

So, I hope you now understand how important our size is for our survival. We are big and scary creatures, and that’s allowed us to hunt and kill and eat meats and make pizzas and build guns and missiles. But we’re not so large that joint damage, eating entire herds of cattle per day, and toppling over and breaking bones would be a daily norm. We’re also not so small either that we can’t take showers or cultivate food. So, here we stand, results of the goal-less, powerful, yet delicate hands of natural selection. Just right.

Nobody comments on my stuff. You should comment on my stuff. Get your friends to comment on my stuff. I will then comment. We can all comment. It will be a great world full of comments.



Literature Sources:

[1] http://en.wikipedia.org/wiki/Kleiber’s_law

[2] “Ever Since Darwin” by Steven Jay Gould, Norton & Co. 1977

[3] http://science.howstuffworks.com/life/inside-the-mind/human-brain/brain-size2.htm


[5] http://journal.frontiersin.org/Journal/10.3389/neuro.09.031.2009/full#B24

Pitcher Plants

“Wish I could use some of your stuff in my classes but it is too ‘mature’ in language.” –My mom, a middle school science teacher.

Mom, the articles are called Badass Biology. These ain’t no cupcake creampuff articles for babies. These are articles for ass-kickers that love facts. I want my articles to cause nosebleeds.

If my articles were plants, they’d be carnivorous. Only, they’d be sneaky and deceptive, luring in readers with the promise of sweet nectar but instead causing them to fall into an unescapable chamber and drown in a vat of literary acid. I wish nature was awesome enough to grant us a plant so wonderful. That would kick ass.


1) They f**king exist.

You know there’s going to be some serious s**t going down when the first item of a list tells you that something exists.

The plants I’m referring to are called acid death plants. I lied, they’re called  trap dissolvey plants. I lied, they’re called pits of agony plants. I lied, they’re called swimmey swwimmey death time plants. I lied, they’re called roses. I lied, they’re called pitcher plants. They encompass a broad and diverse array of plants from many ancestral lineages that contain one common feature: an unescapable pit of doom and death which the plants dissolve, digest, and absorb their unlucky prey. Pitcher plants also have googly eyes, which is pretty sweet.


Pitcher plants come from a variety of locales and lineages. However, all have independently evolved googly eyes.

The pitchers for which these plants are named are actually highly modified leaves, tempered into kick-ass death traps by the will to survive. Called pitfalls, these leaves have three primary zones, all of which are designed to trick insects into letting a plant kill and eat them. Bummer.

 Zone 1: The bait and slip.
The opening of pitfalls contains some kind of delicious bait that attracts insect prey. Baits can include cells that produce nectar, tiny hairs called trichomes that release sweet-smelling chemicals, or parking lots where local food trucks meet to entice flies and ants with Korean-Mexican fusion

But trouble awaits the hungry. When insects land to feast upon barbecued tacos, they land on a slick waxy surface that causes them to slip into the pitfall. Those plantey bastards. However, these waxy coatings are most efficacious when wet; some insects do not slip on this coating when the plant is dry. Even more bastardly is the strategy of Sarracenia flava; the opening is also coated with an insect anesthetic that paralyzes prey and reduces their chances of escape, made unlikely by the next zone…

Zone 2: There is no escape
The walls of the pitfall are structured in a way that makes escape essentially impossible for insects that are either too clumsy or too stupid to figure it out. The plants’ means of accomplishing this task depends on its taxa; some plants utilize downward-growing hairs that make the walls difficult for insects to climb. Others implement waxy scales or folds in the wall tissues. By far, the most interesting is that of some members of the genera Sarracenia (seriously, these guys kick ass) and Darlingtonia. The walls of their pitfalls are lined with tiny aldehyde crystals that hinder upward motion, turning the walls into a beautiful biological Aggro-Crag.

Zone 3: The pit of despair
It’s no surprise that liquid fills the bottom portion of pitcher plants. The main ingredient in this mixture is rainwater, collected by funneling into the pitcher using a series of specialized companion leaves. However, these leaves also act to repel water to prevent inactivation of the second ingredient in this deadly cocktail: rocket swords. I mean acidic digestive enzymes. These enzymes break down any poor prey that falls into the trap, leaching nutrients into the surrounding medium that can be absorbed by cells lining the pitfall. These enzymes are so powerful that they often hurt the plant itself. To counter this, some pitcher plants release additional compounds that form a physical barrier that prevents chemical damage to the inner wall. In other words, these plants are so deadly that they need to protect themselves from themselves, much like a tattoo of the Triforce from the Zelda games protects you from women.

Like a fisherman that like, I dunno, uses his eyes to look at his catch, pitcher plants can also sense how much food they’ve caught. To prevent excess damage to themselves, pitcher plants keep the amount of nasty enzymes low and release a lot more of them once they’ve caught food. Interestingly, the amount of enzyme they release is related to the size of the food item they’ve captured; larger prey causes more enzymes to be released. How do they know? Pfft, I don’t know, but I bet it’s complicated. I’m just going to claim nobody knows exactly how it’s done.

2) The pitchers arose in different groups of plants independently

I don’t know why people think evolution creates “perfect” organisms. That’s not the point, otherwise I’d be able to shoot laser beams from my eyes. Don’t worry, I’d use them for good, like scanning barcodes or calculating the dimensions of a bedroom. However, that’s not how natural selection works. Instead, organisms just need to be good enough to survive and reproduce. These changes are usually small ones, and they’re very infrequent. However, harsh environments can speed up the process by exerting a lot of pressure to adopt a particular adaptation in order to meet these needs.

Sometimes, different organisms adapt similar strategies to survive in their environments. Desert plants are a prime example of this; many have developed thorns, thick tissues, light color, cookie fruits, the ability to change color when frightened, and root systems that are broad or deep because those adaptations work in those tough environments. When different organisms developing similar adaptations, convergent evolution occurs.

That’s also exactly how pitchers developed over evolutionary time. Pitcher plants come from several different taxonomic groups that have all independently developed pitfalls. Not only that, but their pitfalls are strangely similar considering the plants’ diverse ancestry, which presents an added level of elegance to this whole thing.

Convergent evolution; All of these organisms have independently developed the tendency to be gigantic assholes to other species.

3) Their ecology is just so friggin cool

An organism’s ecology describes how it interacts with living and non-living things in its environment. Typically, an organism’s effects on other organisms are more direct and important, so that tends to be what most ecologists study.

Most of the interactions between organisms involve a negative component. Herbivory, predation, parasitism, and competition are all forms of interaction where one or both of the parties suffer for taking part. However, organisms can also help one another by facilitating each other’s growth or reproduction or by providing refuge against competitors or consumers. Interactions where both parties benefit are deemed mutualistic.

Pitcher plants, being the badass acid pits that they are, actually do a lot of good for their communities. Bacteria grow in the pitfalls in high densities, providing nutrients and additional digestive enzymes for the plant in exchange for a suitable place to live and multiply. Small insects, such as mosquito larvae and ants, use the plants as a shelter while helping to speed up digestion of prey. The VFW rents out pitcher plants for Wednesday night bingo tournaments. Weirdest of all, small mammals like rats, bats, and shrews use pitcher plants as toilets, providing much-needed nutrition for the plant while separating the animals from their waste.

What’s coolest is that pitcher plants harbor tiny aquatic communities. As time goes on, some species invade, others go extinct, and so on until the pitcher plant dies. Thus, pitcher plants can act as mini-environments, providing an easy way for ecologists to study how nearby communities can influence one another over time and how they vary across space.

4) I’m done.

5) No I’m not. 

I wanted to restate that these plants are probably some of the coolest non-moving things to have ever not moved. They’re the natural world’s equivalent of a pit of spikes, only they facilitate unique communities and foster the growth of nearby species. They’re like benevolent angels covered in cactus thorns that lie in wait for wicked-hearted brigands to seduce, only to consume their souls the very second they fall into the trap.

Much of the information in this post came from the paper accessible through the following link:

Krol, E, BJ Plachno, L Adamec, M Stolarz, H Dziubinska, and K Trebacz. 2012. Quite a few reasons for calling carnivores ‘the most wonderful plants in the world’. Annals of Botany 109: 47-64

Want to hear me talk about your favorite badass thing in biology? Post it in the comments below!