Gamification for positive habits

For as long as I can remember, I’ve enjoyed video games.  If there’s leveling up, character optimization, or strategic battles to be had, I’m in.  At my worst, I can burn an entire Sunday; I’ll admit that I’ve banned myself from playing DOTA2 after one too many late nights.

At their best, video games can be a vehicle for me to work on my goals.  For example, I’ve been changing the language settings on my videogames to Spanish.  I’m not learning a ton of practical vocabulary, sure, but immersion is a great thing, even if it’s silly.

The vocabulary can be a little silly, but immersion is good.

A newer concept for me is Gamification.  At it’s core, gamification is about turning stuff that you want to get done into a game.  Duolingo is a simple example of this.  Complete vocabulary lessons to level up and unlock new lessons.  When accomplishing tasks results in leveling up and earning rewards, the same compulsion that lead me to waste my teen years playing Everquest will now work in my favor.  That’s the idea, at least, and I manage to keep up with Duolingo fairly well.

Duolingo tracks your daily language progress through experience points (XP).   The site encourages you to make progress every day.  Looks like I'm not too consistent this week.
Duolingo tracks your daily language progress through experience points (XP). The site encourages you to make progress every day. Looks like I’m not too consistent this week.

HabitRPG is MUCH more ambitious with this concept.  It goes all out, giving you an avatar with the ability to earn mounts, group up with friends, and fight bosses.  You get to choose your “quests” so it can be tailored for whatever purpose you’d like.  If you set a daily goal to study for one hour, you’ll gain experience points and gold for completing it, but take damage each day you feel to check it off.  You can then spend accumulated gold to buy rewards that you specify, or in-game swag.

HabitRPG takes a fantasy RPG approach to positive habit building.

There’s no doubt that consistency and repetition are the keys to setting up positive habits.  This is where a tool like HabitRPG shines- it rewards positive habits in a fun and imaginative way.

I’m setting up my HabitRPG account to encourage more productive use of my free time.  In a future blog post, I’ll reflect on how gamification can be used in the laboratory.

Who are CyberVor?

Well, the BBC and The New York Times have both published pieces on the Russian hackers “CyberVor”.  The claim is that  1.2 billion user names and passwords from some 420,000 websites have been hacked.  The sites/users affected, nature of the vulnerability, and severity of the threat have not been disclosed.

Skeptics have pointed out that, well, things don’t really add up.  The biggest problem is that The New York Times was fed the CyberVor piece by Hold Security firm.  This is the very same firm that stands to profit from this security breach, by charging $120/year for their services.  The New York Times piece, to my eye, does not validate the information provided by Hold Security.  The truth is that its in Hold Security’s interest to exaggerate the breach, and in The New York Times’ interest to report the story as quickly as possible.  Without released facts or data, this entire story could have been fabricated by Hold Security.  This is unlikely, as The New York Times piece claims that two unaffiliated sources verified the database as authentic.  Still, experts seem to think the threat could be exaggerated.

So what does Hold Security know about CyberVor?  According to The New York Times piece (which means according to Hold Security, who sell the solution to the CyberVor problem), CyberVor is made up of fewer than a dozen men in South Central Russia.  Hold Security knows this because they have been in communication with them.  Seriously.

CyberVor: we know they are real because we Skype all the time.

I’ll be interested in seeing how this develops.  As it is, I see a lot of big claims with no evidence or specifics, and the group making the claim profiting from the resulting panic.  I also find it odd that CyberVor and Hold Security communicate.  Is that normal?  Do hackers usually chat with data security firms?  I can’t even verify that CyberVor is a thing from anyone other than Hold Security because, well, Hold Security coined the term CyberVor, and that is all we have to go on.

As other skeptics have advised, however the threat plays out, taking cyber security seriously is a wise decision.  I recently invested in password management software, and highly recommend it.


Scientific writing is dry (but that’s OK)

This morning I was delighted to come across the IMA Fungus journal.  Put out by the International Mycological Association , the journal title (which primarily publishes species announcements and descriptions) playfully introduces each organism with a friendly “Hello, I’m a fungus!”  The truth is, scientific literature is seldom so fun and informal.

When I submitted my PhD dissertation draft to my committee, perhaps the most common complaint I got was that I was having too much fun with the writing.  Given the choice, I  always prefer to be playful than bland in my writing.  In science, this isn’t necessarily a good thing.  Primary scientific writing values clarity and correctness.  In trying to evoke vivid descriptions, I like to describe science with flair, pushing my metaphors to the absurd.  For example, I wrote that fungi forge weapons to wield against the parapets of plant defense, or that they brew novel molecules in musty cellular laboratories.

The problem is that while I have a lot of fun writing statements like this, it empowers organisms with sentience and intent.  It is incorrect.  So such statements are refined to purge embellishments (fungi produce molecules that specifically target host defenses, and produce diverse secondary metabolites in specialized cellular structures).

Me being dangerously informal during my exit seminar.
Me being dangerously informal during my exit seminar.

Obviously we should strive to be correct in our communication of science.  When publishing, it must be clear what we did, what we observed, and what we believe these results mean.  We must write knowing that english is not the primary language of those who are interested in our experiments.  But does this mean that we can’t have any fun?  I can’t speak for all scientists, but my love of biology is not sterile and precise.  It is colorful and messy.  It is most certainly anthropomorphized (despite my higher faculties being well aware that fungi are not sentient creatures).

We scientists are a fun bunch.  This fact is more than evident from any academic conference (take the raging party that is the Fungal Genetics Conference).  But our writing is often denser than German fitness bread.  Maybe it’s impossible to get away from that in our formal writing without introducing ambiguity or compromising our professionalism.  I suppose some day I’ll find out.

How many copies of my thesis/dissertation should I order?


You’re finished!  You’ve spent hours writing and rewriting your thesis or dissertation (such semantics!), braved your defense, and spent even more time addressing your committee revisions (to say nothing of the years of hard work that got you here).  Congratulations.  Time to submit and watch Buffy the Vampire Slayer for eight days straight, right?

This sums up my feelings on graduation nicely.
This sums up my feelings on graduation nicely.

A couple of issues I hadn’t thought about came up before I clicked submit, however.  One of these was how many copies of my dissertation I should order.  I had no clue, and I was pretty braindead by this point.  So I thought I’d list some people who might want a copy for future generations of sleep-deprived and deadline flaunting scholars.  If you forget somebody, that’s OK- I was able to re-order a single copy for ~$80.


Your parents, and perhaps grandparents, are a given.  After 4+ years of not being able to explain your work to anyone, having a 5 pound coffee table book to gesture at is going to make their day.  Don’t forget to include them in the acknowledgements!


I didn’t order a copy for any friends, but that doesn’t mean you won’t want to.  Finish before a friend who started the same year?  Nothing rubs it in their face quite like a printed copy of your dissertation.  It sure is an expensive snub, though.

Your advisor

Do not forget a copy for your advisor.  Again, write something nice in the acknowledgements or pay the price.  I learned the hard way that “To my favorite advisor” isn’t acceptable.

Your committee

Did you receive a lot of guidance from your committee, or shed a lot of tears in their office?  This can be a nice gesture of thanks.

I keep my thesis on my person at all times (if only to stop bullets).
I keep my dissertation on my person at all times (if only to stop bullets).

Your lab

This is the one place where someone might open your dissertation for very practical purposes.  Over the course of my time at Cornell I’ve consulted the dissertations of others surprisingly often, be it for a unique perspective on the literature or to see the nuances of methodology not written out in peer-reviewed publications.

The library

Your campus library probably prints a copy of your dissertation for its own purposes, but its worth checking that this isn’t expected of you.  How else could you perform the infamous $20 experiment, hiding a crisp bill in the meat of your dissertation and returning year after year to see if its disturbed?  Also, some departments keep separate dissertation collections- see if you are expected to contribute!


This probably goes without saying.  You may feel like you never want to see this cursed book again, but you probably will.  Even if its only to drag it out as a war story, or to prove to your date that you really can run a southern blot.

Celebrity burgers a reality

Back in September last year, I explored some possibilities that the “Stem Cell burger” opened up.  Perhaps the most far-fetched idea I had was to produce meat from cloned celebrity stem cells.

It seems this idea wasn’t as absurd as I thought.  A new company has launched called Bitelabs, claiming they will produce celebrity-derived meats in salami-form.

Always push the boundaries in taste

So is it a hoax or a real company?  The internet isn’t quite sure what to make of it.  My previous post covered the feasibility of such an endeavor, but the ethics remains a gray zone. In the meantime, I fully support the discussion, and I applaud Bitelabs’ understated strategy.  Personally I’d be interested in trying a cloned meat product, regardless of who the donor was.

Consider the ostracod

What does it mean to be a scientist?  I present to you some overly poetic thoughts on the topic.

It was a soggy morning in early Fall when I encountered an ostracod.  I had just submitted my dissertation, I was unsure about my future, I was exhausted.  To celebrate, I went hiking with a party of undergraduate and graduate students led by the intrepid Kathie Hodge foraging for mushrooms.  We had chased the rain but missed its fungal fruit, finding only a small handful of mushroom gold, Chanterelles.  We decided to return home, and on the walk back,  came across puddles housed in muddy tire tracks.  They were teeming with tiny life.  The sleek tadpoles, buzzing flies, and squirming larvae held our attention for a while, but we soon spotted a most unusual creature.

Laying still, it looked like a small pebble the size of a grain of rice, its surface coated in slimy mud.  Careful observation found that the pebble scooted around the puddle in small circles, propelled as if by an onboard motor.  Enthralled, I plucked one and teased it on my finger.  What was this microscopic backwoods clam?  Amazingly, a tiny shrimp-like head poked out, with sweeping tendrils.  I immediately announced we had discovered a lost species of clam-shrimp, and found a nearby coca cola bottle to collect one.  Before we could gather another, an ATV rode by, crashing through the puddles and hopelessly clouding our view.

Arriving at the lab, we armed ourselves with a microscope, and the knowledge of the scientific community.  Kathie immediately decided we were dealing with an ostracod.

An ostracod. Photo from Wikipedia:

Observing our ostracod (we named her Sue) scooting around under the microscope was a joy.  My curiosity for Sue was fed by an excellent website by Robin James Smith at the Lake Biwa Museum.  I highly encourage you to visit Robin’s website, especially the images section (I’ve included my favorite sketch below).  Amazingly my initial assessment wasn’t far off: the common name of my “clamshrimp” is actually “seed shrimp!”

A sketch of a female ostracod, by Robin James Smith

The amazing thing about biology is that a simple walk through the woods can ignite an entire afternoon of looking through a microscope and learning something new and bizarre.  I now know that ostracods can produce spermatozoa up to ten times their body length, can be bioluminescent, and can hunt in groups!  Every organism has an untold story, with so much left to learn and be discovered.  And thanks to the unbelievable scope and rigor of science, a discovery can easily climb the scaffolds of human knowledge.  We can just as easily reach the peak, and wonder at the reality just beyond our comprehension.

I don’t think one needs a PhD to appreciate the beauty of the world.  Anyone who is excited to explore life, big or small, is a scientist in some way.  The life of a ‘real’ scientist is filled with lab notebooks, presentations, grant proposals, budget forms.  But these things are carried out in exchange for that spark of wonder that can be found in a muddy pond in the woods, in our blood, or floating in the Atlantic.

Ethical implications of the Stem Cell Burger

I am  writing a short piece on the Stem Cell Burger which was unveiled early last month.  The Cultured Beef website is eager to point out the many benefits this technology could have for global research usage and animal ethics.  Opponents are just as quick to point out the possibility of unknown side-effects.

An animated video of how the burgers are grown from cultured cells.

Cultured Beef may change the world- but maybe not in ways people expect.  I’ve jotted down a few of the more extreme implications for Cultured Beef.  I’m not an actual proponent of all these ideas: this is really just a thought experiment for possible ethical issues downstream of culturing just beef.

1)  Eating endangered species.

Why limit ourselves to cows?  If we can string together cow cells grown in culture, why not the cells of a Bald Eagle?  It would be arguably the most American burger possible, and wouldn’t require death or suffering from of our favorite bird of prey.

Bald Eagle Burger is a real band!  The burgers aren't real.  Yet.
Bald Eagle Burger is a real band! The burgers aren’t real. Yet.

2)  Eating extinct species.

With scientists pondering the implications of cloning extinct species, such as the woolly mammoth, why not clone these extinct species into the Cultured Beef pipeline?  I imagine lots of people would be very excited to eat woolly mammoth burgers.

Mammoth ribs, the original family meal.
Mammoth ribs, the original family meal.

3)  Eating people.

Cannibalism is one of those taboos that people love to joke about, but when push comes to shove, few in our modern society would seriously consider.  But what if there was a meat you could buy that came from people, without anyone being hurt or killed?  And we aren’t just limited to eating any old person.  Cultured cells of celebrities, dead and living.  Bill Clinton hot dogs.  Miley Cyrus patties.  American celebrity culture is ready.

Forget energy drinks, stem cell burgers could be the next big endorsement.

4)  Eating ourselves.

Why stop at eating other people?  We could custom-sell Cultured Beef to be made from an individual customer’s cells.  Depending on the source of broth nutrients, this could be an entirely new movement in veganism.  No more annoying jokes about murdering vegetables.  I’m 100% self-supporting, subsisting on only genuine Me-burgers grown in bacterial broth.

Note that I don’t condone cannibalism, or Miley Cyrus, and I think that Cultured Beef is a great idea.  What about you?  If you could culture an organism’s cells and eat them, what would you pick and why?