Category Archives: Biology

Bill Nye the Science Guy meets Vin Can the Science Man

OK, so I need to work on my stage name.

Back in May 2017, I tweeted at Bill Nye:

And it turns out that Bill, and the great writers and producers and everyone else behind Bill Nye Saves the World, were paying attention. Shortly after the tweet I was contacted by a producer of the show and asked if I would like to come on and give a demonstration about the evolution of “super-bugs”, i.e. antibiotic-resistant bacteria.

An opportunity for science outreach involving Bill Nye? Yes, please.

In this post, I first want to talk about the science in my 5 minutes (at the end of Season 2 Episode 3 of Bill Nye Saves the World). Then, I’ll touch on the experience of being on the show.

The Science

I wanted to convey three things in my demo:

  1. Antibiotics work really well!
  2. So does natural selection. In the presence of an antibiotic, bacteria resistant to that antibiotic survive and proliferate more than non-resistant bacteria, leading to the spread of the information conferring that resistance (i.e. the evolution of “super-bugs”).
  3. And that’s why it is important to be judicious about antibiotic use.

all while conveying how scientists can use models of reality to study biology.

So, for my demo I created a model of the evolutionary dynamics of bacterial strains within a person. In this model, bacteria either replicate or die—similar to a common mathematical model used to study evolutionary dynamics called a “birth-death process”. If there is more birth than death, the bacteria grow too big and overflow from the host—the infection spreads to other hosts. If there is more death than birth (as in a typical situation where the immune system does a good job), the bacteria die off —the infection is cleared.

What makes this a model of evolution is that we can introduce two different bacterial strains into the model and observe how the relative abundance of these two strains change within the total bacterial population over time. Let’s say one strain has a mutation in their genome that makes them resistant to antibiotics, and the other strain is still susceptible to antibiotics.

Let’s also assume that the host’s immune system is compromised, all strains are growing more than they are dying. The person goes to their physician, and gets some antibiotics that decrease the birth rate of only the susceptible strain. Growth of the susceptible strain is stopped, but the resistant strain grows and grows, and when the model “overflows” it is the resistant strain that spreads to other hosts.

By continually providing selective pressures favoring resistance, we drive susceptible strains to extinction. As the model suggests, we would expect the spread of antibiotic resistant bacteria to be especially prevalent in areas that have a high concentration of individuals with compromised immune systems that take antibiotics, such as hospitals and nursing homes.

But, there is hope! Many of the mechanisms of resistance are actually costly to bacteria when antibiotics are not present. It may be possible to reverse many of the mechanisms of resistance (select for non-resistant strains) by being extremely judicious about when to apply antibiotics. The original focus of the demo was on how to reverse resistance through exploiting this cost of resistance, however due to time constraints I refocused on the emergence of resistance.

My Experience

Everything was awesome. I had no idea just how much went on behind the scenes to get a show produced. From the props people helping with my demo, to the writers and producers working around the clock anticipating every little thing that will happen. Everyone really cared about being true to the science and explaining the information in an accessible and exciting way. Especially Bill Nye, who was extremely genuine and kind throughout the whole experience. I’m very grateful for the opportunity to help #savetheworld!

20170720_202332

 

P.S.

For those who arrived at my blog curious about my current research: I use mathematical models and simulations to investigate how tumors evolve from our tissues, how evolution has structured our tissues to minimize the risk of cancer, the effects of mutations in growing tumors, and how cancers evolve resistance to chemotherapy. Relating to pathogen evolution, during graduate school, I was part of a team that used mathematical models to study the evolutionary dynamics of pathogens and their hosts.

Advertisements

Dark selection from spatial cytokine signaling networks — Theory, Evolution, and Games Group

Check out a post I wrote over at the Theory, Evolution, and Games Group blog on some of our work at the 2016 Integrated Mathematical Oncology (IMO) Workshop! The link for that post is at the bottom of this post.

It details a really neat model we created to interrogate a system of cytokine signaling and cancer treatment. For those unfamiliar with the IMO Workshop/competition, five teams of a dozen or so researchers, all from different backgrounds, are formed at the beginning of the week, and quickly decide on an interesting research problem they can tackle. Each team has a few physicians and scientists stationed at the Moffitt Cancer Center, where the competition is held, that act as mentors. The groups spend the four days working and researching and planning ahead, and on the last day they all present their completed and proposed work. Oh, did I mention that $50,000 of future funding is on the line? The winning team gets the $$ to complete their proposed research.

This sets the stage for an awesome week-long hackathon, where longer and longer workdays culminate in an inevitable all-nighter as mathematicians and computational biologists and physicians and new colleagues perfect their models and presentations.

So, there we were, 35 hours or so away from the final presentation, when we all decided we needed a spatially-explicit model of cytokine diffusion and cell response. I had created spatially-explicit simulations of cell turnover before, so I volunteered to lead the analysis. And, like the scientist in an action movie rushing to find the vaccine for the zombie virus before the meteor strikes (or something), I worked overnight in my hotel room, and all the next day, and delivered this video and results right before the final presentation:

(For more information on what the video is showing, check out the post linked below or our preprint.)

It was only 2 slides worth of work within our whole presentation, just to give you a sense of how much everyone in the group accomplished during the week. But it was actually a ton of fun rushing to get everything together and connected. And, we won the competition!

imo2016_teamorange_awardphoto

Greetings, Theory, Evolution, and Games Group! It’s a pleasure to be on the other side of the keyboard today. Many thanks to Artem for the invite to write about some of our recent work and the opportunity to introduce myself via this post. I do a bit of blogging of my own over at vcannataro.com […]

via Dark selection from spatial cytokine signaling networks — Theory, Evolution, and Games Group

How much energy is in a thought?

Sometime during the last months of grad school I was in the office late, polishing off one too many coffees, and dipping into my emergency ramen noodle stores. I was searching for that elusive (and perhaps illusory) moment of clarity that, one hopes, arrives to propel a manuscript forward. But, the long hours and coffee caused my mind to wander into distant realms of science. I had just finished teaching about neurons and action potentials and brain activity in my physiology class (100 billion neurons, forming 100 trillion neural connections—more connections than stars in our galaxy—sparking up right now allowing you to think this!) and I had a cool thought:

I am converting these cheap noodles directly into science and new insight. I am a biochemical machine that converts packs of 10 cent fake noodles into knowledge.

And then, the natural follow-up: at what rate? What is the cost of a thought? How many noodles does my brain burn to construct a statement? A paper? A dissertation?

Now that I do not have a dissertation submission deadline looming, I have some time to explore these thoughts—thankfully while burning some higher-grade fuel than emergency ramen! Warning: the calculations that follow are extremely ‘back of the envelope,’ and should be taken with a heaping helping of salt and skepticism. This is just a fun exploration.

How much energy is burned in a thought?

First, let’s gather some parameters. How much energy does the brain use? The short answer is: an incredible amount. Despite only accounting for 2% of the body’s weight, the brain uses 20% of the body’s energy (that figure is for an adult, in newborns it is 44%!!) The brain uses 2–3 times the amount of energy that the heart uses.

[Aside: the brain is extremely efficient at what it does—processing information using orders of magnitude less energy than the best supercomputers.]

So, let’s say that the brain uses 20% of the body’s basal metabolic rate, and the basal metabolic rate is 1500 kcal/day. That means the brain uses about 300 kcal/day, or 0.0035 kcal/second.

The next question is: what is a thought? How much time does one take, and what proportion of the brain’s energy is devoted to “thinking”? I don’t know! But, does anyone know? I don’t know that either. Since it is my blog, I am at liberty to define a thought. Let’s say, for the sake of argument (and feel free to argue in the comments) 100% of the brain’s energy is required for “a thought,” and all thoughts are created equal. And let’s also say that a thought is a statement, and that it takes as much time as one would take to think or read a sentence. For instance, here is a thought:

“Wow, I am thinking this thought about thinking; this is one of the things that hydrogen atoms do given 13.82 billion years of cosmic evolution, and it’s super cool.”

How long did it take to think that specific (extended) thought?  More than a couple of seconds, less than 10? Let’s say a substantial thought takes 5 seconds. At 0.0035 kcal/second, that’s about 0.02 kcal/thought!

So, how many ramen noodles are burned for a thought? At 400 kcal per block, and 150 noodles per block, we have 2.67 kcal per noodle. Assuming the average noodle is 33 cm long, we find that there are 0.08 kcal/cm of noodle—and every thought burns about 0.25 cm of ramen noodle! Your brain is incredibly efficient—no wonder that future AI are always super jealous and vindictive in sci-fi movies.

Now we can readily convert thinking-time into calories, and content creators can register their influence in energy. For instance, if 100 people read this blog post, consuming 5 minutes of calories thinking through the content, then about 100 calories would be burned on my words. 400 people and an entire block of ramen has been consumed by my words.

I wonder how much ramen has been burned by Shakespeare?

My spot, your spot.

I grew up on an island with seven million other people. Let’s just say it was difficult to find a spot to call your own. One day, as a youngin’ exploring the world on my bike, I broke off a path that ran along Sunrise highway and continued on down a hiking trail that snaked along a waterway in the local state park. I eventually came to a small clearing, sat down, and heard the weirdest thing. Nobody. No cars, no lawnmowers, no people. Just the birds and the chipmunks and the occasional splash of a fish.

IMG_20170606_184007_963

I felt as if I had stumbled on secret treasure. I spent a lot of time at this spot over my formative years, reading and thinking and being alone with my little patch of Long Island wilderness.

Before I left town for college I carved a “V” into the tree next to the water and said goodbye. While at college, I decided to major in biology, a decision shaped by my time out in the woods watching nature. I even wrote an essay about this spot for my freshmen writing class.

That biology major took on a life of its own, turning into an adventure through states, labs, and disciplines, and eventually resulting in a PhD from a zoology department and a dissertation on cancer and aging.
Last weekend Begum and I were visiting my parents and we decided to go for a quick hike before the ferry back to CT. A rush of memories came back, and I ran along this trail explaining my spot to her. She eventually found the V for me.

IMG_20170606_184007_962

Both of these images are from June 2017

It was the first time in over a decade that I set foot in this clearing. Needless to say, it was a powerful experience, and it sparked a bout of retrospection that, thankfully, I have been happy to ride.
I said a thank you, and another goodbye, and we ran to catch our ferry.

This summer, I hope you go out and explore, and find your own spot.

Spider Sunday is back! Kind of.

Spider Sund… err… Monday is back!

Back when we lived in Florida, stumbling on cool spiders was easy. Just open your door, take a few steps, and BOOM, golden orb-weaver (not to be confused with a yellow garden spider) taking care of your wasp problem. Or role out of bed to discover your new roommate, a Carolina Wolf, is on the prowl for mice (I presume). Maybe she’ll even bring along her closest 100 kin.

But New England, with its “seasons,” is a different story*. So, imagine my surprise and delight when Begum and I were hiking around Farm River State Park and saw this little fella scurry across the path:

20170610_131039

At Farm River State Park, CT. Picture taken with Galaxy s7. 

After some quick searches, I outsourced my initial guess to the amazing sciencesphere of twitter:

@HereBeSpiders11 with the save! Looks like this is a type of ground spider (we did find it on the ground), specifically it looks like a male Sergiolus capulatusThanks!

Some suspect that the awesome pattern may be an adaptation to mimic the velvet ant (which is actually a wingless wasp), known for their extremely painful stings!

Looking forward to what we find on our next hike.

*Actually, maybe it is not such a different story. Looks like we will just have to be more attentive on our next hike!

Want to find life on Mars? There’s a catch…

There has been a lot of talk recently about “getting our ass to Mars” (to phrase it as Dr. Buzz Aldrin has on social media). Whether it’s Elon Musk talking about the new SpaceX plan to colonize Mars (first passengers might be taking off by 2024, start saving!), the record low global sea ice levels here on Earth, or just the results of recent elections (Fig. 1) — people have been thinking about extraterrestrial adventures.

screen-shot-2016-12-27-at-1-50-08-pm

Figure 1: Google Trends for “I dont want to live on this planet anymore” searches. November 8th 2016 was election day in the USA.

This gives me a good excuse to share one of the most interesting challenges we face when finding a landing spot on the Red Planet.

Surely, when sending a Rover to Mars in search of life, like we will in the year 2020, we would want to send it to the place that is the most likely to harbor life (or has the ingredients necessary for life according to our understanding of what life requires here on Earth). Right? This is probably true for when we want to send humans there as well— the more similar to Earth, the higher our chances of survival. But, there is a catch.

The site we think would be the most likely to harbor life would also be the most likely to be infected with life from Earth­— life that could outcompete the local Martians and lead to a planet-wide extinction. We (or, our microbes) could be the classic Hollywood alien invaders who annihilate local life in the search for resources.

Now, someone who has never read this blog or sat through a microbiology class might think “Hey, easy solution, just sanitize things before takeoff! Plus, the harsh conditions of space travel will get rid of any pesky stowaways.” Not so easy.

Firstly, let’s pretend for a moment that our bodies are not harboring a complete ecosystem of microbial life, and that somehow we can guarantee that humans and their waste never contact the surface of Mars. Still, microscopic life is everywhere on Earth. And I mean everywherelike 800 meters below the ice in an Antarctic subterranean lake everywhere. I think it is safe to say that some of this life will contaminate anything we send to Mars. In fact, 65 species of bacteria were found stowed away on the 2012 Mars Curiosity Rover.

Secondly, some microbial Earthlings are extreme. And I mean extreme— like proliferating at 403,627 × Earth’s gravity extreme. Like living in a liquid asphalt desert extreme. And yes, like living outside in space for 1 and a half years extreme.

So, the possibility of microbial stowaways surviving to mars is real.

And, of course, NASA knows this. In fact, they have a whole Office of Planetary Protection devoted to, among other things, “Avoiding the biological contamination of explored environments that may obscure our ability to find life elsewhere – if it exists; …”. The United Nations knows this as well. The Treaty on Principles Governing the Activities of States in the Exploration and Use of Outer Space, including the Moon and Other Celestial Bodies includes:

States Parties to the Treaty shall pursue studies of outer space, including the moon and other celestial bodies, and conduct exploration of them so as to avoid their harmful contamination and also adverse changes in the environment of the Earth resulting from the introduction of extraterrestrial matter and, where necessary, shall adopt appropriate measures for this purpose.

The possibility of contaminating planets that may harbor life presents a real ethical dilemma for robotic and human colonists. Should we search out life on a planet surface and also risk infecting the planet with Earthling microbes? Should we colonize another planet if it means we may destroy the local inhabitants? I’m not going to try and answer those questions here, but feel free to leave thoughts here or tweet them to me.

Spider Sunday is back! This week: Wolves in Your Backyard.

I have a confession. When I was young I wasn’t very kind to spiders. My behavior can likely be attributed to fear; growing up we are surrounded by imagery of spiders being dangerous and alien. We fear what we don’t understand. The internet says Marie Curie once said “Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less.” And it’s true, the more I learned about spiders the less I squashed them. Now that I’m older, and a biologist, and living in Florida (read: constantly surrounded by giant spiders), I see spiders as fascinating, useful, and largely innocuous. And I’m on a mission to spread this view in order to gain back all the biology-karma I lost squashing spiders in my childhood. So, here are some neat facts I just learned after to a recent encounter.

Storytime. The other night I was outside enjoying the (relatively) cooler Floridian night and getting some work done. Suddenly I glimpsed a familiar shape darting towards the leg of my chair. A few inches long, but too meaty and agile to be an orbweaver or banana spider, I knew it had to be a wolf spider. So, I jumped up and reached for my phone and rushed to snap a picture before she retreated. When the flash went off I was greeted with a surprise…

Proud Wolf Spider Momma

Proud Wolf Spider Momma

Reflections. Reflections from eyes. But wait, why are there reflections coming from the spider’s abdomen?

Woah. Cool! Ok, so now I know that wolf spider’s eyes are reflective, just like I’ve seen (and posted about) before in Golden Orb-weavers…

20151014_115941

Golden Orb-weaver, La Chua Trail, Gainesville FL.

This is very similar to the reflections we’ve all seen before when shining a light towards certain mammals at night, such as cats or raccoons.

Raccoon hanging out behind UF's Science Library, Gainesville FL.

Raccoon hiding out behind UF’s Science Library, Gainesville FL.

So, what’s going on here? By reflecting light back through the retina there is more light available to the photoreceptors- enhancing night-vision. In vertebrates this is accomplished by the tapetum lucidum, or “bright tapestery” in Latin, a thin tissue membrane in the back of the eye. It looks like the tapetum has evolved independently in invertebrates and vertebrates, and actually exists in several invertebrate taxa including scallops, crustaceans, scorpions, and dragonflies. The tapetum in invertebrates consists of parallel strips of reflective guanine crystals- the same type of crystals that give fish their shiny metallic skin and allow chameleons to shift their skin color.

Want to see it for yourself? Go outside at night and shine a bright light into the grass. Those hundreds of reflective dots shining back? Wolf spiders looking at you. But fear not, for now you understand more. Just wear shoes.

(and share your cool spider pictures with me!)