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!

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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

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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?

Spider Sunday, Puerto Rico edition

We had an amazing time recharging our science batteries and exploring the island of Puerto Rico for a few days this August:

We spent much of the vacation out and about in Nature, meeting new (to us) birds and frogs and lizards, and some really cool plants.

via https://en.wikipedia.org/wiki/File:Mimosa_Pudica.gif

One surprising find was seeing our old friend, the golden orb weaver. We even saw one outside the Cueva Ventana that had succumb to a fungal infection of some sort:

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Dead Golden orb-weaver. Check out the fungus growing out of the leg joints.

I showed this image to a mycologist friend and they thought the fungus may be from the genus Beauveria. In all of my years living in orb-weaver infested Gainesville FL, I have never seen a dead banana spider!  Had to share!

 

 

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.

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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.

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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:

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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!

Roadtrippin’ with my favorite ally

Begüm gave me a GoPro camera as a gift for submitting my dissertation (because I live such an #extreme life). We put it to good use and made a timelapse of our travels from Florida to New England! I think it came out pretty cool, check it out:

There is no audio—I recommend choosing your own song. On a related note, we had our playlist on shuffle and “New York State of Mind” by Billy Joel came on right when we reached the Verrazano bridge. It was a pretty powerful homecoming moment for this Long Island kid. And then it started raining pizza and bagels (ok, I made that part up.)

Our route:

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Gainesville, FL –> New Orleans, LA –> Atlanta, GA –> Savannah, GA –> Raleigh, NC –> Philadelphia, PA –> Long Island, NY –> New Haven, CT –> Boston, MA

 

Many many thanks to our friends Scott, Dorian, Kevin, and Rich and Amber who hosted us along our journey. During graduate school we always daydreamed about taking a roadtrip after we finished up, and you really made it possible for us.

Begüm is the family photographer, so I don’t have many images to share. But, here are a few scenes from the road.

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All packed up saying goodbye to our little apartment and our little garden.

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Watching the ships roll by in New Orleans.

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Meeting some new friends in Atlanta.

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And some old friends.

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Watching the dolphins, Savannah, GA

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Becky helping us unpack, Long Island, NY

 

We hope to fill out that map with more trips in the near future! Next up: Cannataros head West (Geneseo, Niagara Falls, maybe some Canada adventures).

p.s. Dear Upstate NY friends: We are willing to trade delicious homebrew in exchange for lodging.

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.

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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.