Tag Archives: science

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

Posted on November 30, 2017 | Leave a comment

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

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How much energy is in a thought?

Posted on October 15, 2017 | 7 comments

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?

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Posted in Biology

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The Ultimate Sunset

Posted on May 4, 2014 | 1 comment
April 15, 2014 03:49am

April 15, 2014 03:49am

I took the telescope out during April’s lunar eclipse…

20140415_022302

April 15, 2014 02:23am

… and had a really amazing time. At first it was just the mosquitoes, the clouds, a cool drink, and myself, but after a while people started pouring out of their apartments to see the show.

April 15, 2014 01:18am Staying homed in with the laser finder, waiting for the clouds to leave.

April 15, 2014 01:18am
Staying homed in with the laser finder, waiting for the clouds to leave.

So of course I invited them all over to watch through the telescope. By the end about 10 strangers were standing around watching the bloodmoon and discussing human history, space, science, etc.

April 15, 2014 12:54am

April 15, 2014 12:54am

Imagine what it would be like not knowing anything about the true nature of eclipses and, one seemingly random and unpredicted night, the full moon started disappearing- and then turned blood red. What a sign!

Luckily, we live in a time where humans have walked on the moon, so we do know a bit about it. So, why does the moon turn red?

Well, what color is the sky? (class shouts blue!) If the sky was blue, then how come images of the Earth from space aren’t of a blue ball? Or we don’t normally see a blue moon and blue stars? The sky appears blue because our atmosphere scatters blue wavelengths of light more than other wavelengths of light. When the sun is low in the sky, like during a sunset, the light reaching your eyes has passed through much more atmosphere than when the sun is high in the sky, causing most of the blue light to be scattered out already (for people who are experiencing noon elsewhere). So all that’s left in the light when it reaches your eyes during a sunset are the yellows and reds.

During a lunar eclipse the moon is behind the Earth, with the sun on the other side. The light reaching the moon has passed through the edges of the Earth’s atmosphere, causing a projection of what we see in a sunset to fall on the face of the moon. It’s the ultimate sunset!

 

Open question: Alright, after reading some Wikipedia articles on diffuse sky radiation and the like… I have a question. If our atmosphere scatters blue light, and images of the Earth from space are possible because sunlight is being reflected off of the Earth’s surface and into a camera, how come the Earth doesn’t appear reddish? You know, since the sunlight has passed through the atmosphere twice (down to Earth and back up to space?)

 

p.s. here’s a paper from 1868 “On the blue colour of the sky, and the polarization of light“

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Posted in Astronomy, Fun Fact

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1.1 Billion

Posted on January 23, 2014 | 1 comment

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

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

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

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

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

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

lifetime

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

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

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

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

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Posted in Biology, Uncategorized

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Flocking Science

Posted on January 19, 2014 | Leave a comment

Check out the beautiful video below of a “murmuration” (flock) of starlings acting in hypnotic unison:

Now, if you spend all day thinking about how to model biological systems (who doesn’t?), you might see that video and wonder about the rules each bird must follow to allow such spectacular emergent dynamics. Every individual bird probably gets some simple cues (direction, speed) from its neighbors, who get some from their neighbors (and that first bird), etc etc, and when these simple cues are acted upon and combined together all the birds form a giant complex morphing swarm.

A quick search reveals that the starling dynamics, and swarming behavior in general, have been the focus of a considerable amount of research and modeling. I’ll link this PLoS ONE paper since it’s open access (meaning everyone can view it in its entirety for free) and has some really cool videos showing off the modeling endeavors of the authors. In their simulation, each individual is characterized by parameters like mass, speed, position, and orientation- and these parameters get updated based on interactions with other individuals within a certain neighborhood. Just like in real life, these simple interactions scale up to show a swarm of individuals that behave as a complex, yet unified, group. (check out the videos in the link!)

I’ll also share this PLoS Computational Biology paper (also open access) which explores why individual starlings pay attention and respond to exactly seven of their neighbors (the authors report the number is special because it optimizes the balance between group cohesiveness and individual effort).

Another side effect of thinking about biology all day is always having to ask “Why (and how) did this evolve?” That is, what benefit does this intricate dance give the birds that allowed it to selected for and maintained? Being relatively ignorant of birds and their behaviors, it seems that such a show would turn into a buffet for predators. Well, maybe not. Here is a video of a Peregrine Falcon trying to snatch a starling during the flocking behavior and continually coming up empty handed (clawed?). The Peregrine Falcon is the fastest member of the animal kingdom, reaching diving speeds of over 200mph, so maybe this dizzying behavior is a great way to confuse even the quickest of predators.

I’m sure there is more to it than just predator avoidance, so feel free to add your 2 cents below!

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Cool weather

Posted on January 13, 2014 | Leave a comment

The recent cold snap across the U.S. dusted off some neurons that hadn’t been used since Earth Science- and in the process I made a pretty cool (lol) connection with some images of Saturn recently released from NASA. The Earth has a vortex of cold air spinning around its North Pole, and in early January this vortex branched out and dropped a blanket of cold air onto the Americas.

Image Image

As you can tell from the above images, our polar vortex isn’t especially consistent or symmetrical in shape. The same can not be said for Saturn’s polar vortex…

Image

Credit: NASA/JPL-Caltech/SSI/Hampton University

The beautiful series of images above was taken from the Cassini spacecraft. “The hexagon”, as it’s known, has a hurricane at its center with cloud speeds of 330 miles per hour.

Image

Credit: NASA/JPL-Caltech/SSI

It’s awesome to see well-documented phenomena on Earth taken to their extreme on foreign planets. Hopefully we’ll see more as we continue to explore the worlds in our solar system and beyond.

Check out more stunning images of the hexagon here.

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Image

Carolina Wolf Spider

Carolina Wolf Spider

Hogna carolinensis, found in my apartment, Gainesville, FL.

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Posted on October 21, 2013 in Uncategorized

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The Second Most Astounding Fact

Posted on October 12, 2013 | 4 comments

“The Universe is within us”

Alright, I can’t compete with Neil deGrasse Tyson’s fact for #1. But, I do know the second most astounding fact. There is a biological universe within us. Well, more like an ecosystem. A planet. Where interplanetary travel and colonization are possible. I’ll explain.

Lets consider “you” the planet. And by “you” I mean the ~30 trillion cells that you are comprised of that have “your” DNA- the cells that make you “you.” Now, your planet has many inhabitants that aren’t “you.” Entire communities that have colonized different parts of your body and work in harmony (synthesizing vitamins, aiding in digestion, etc.) with the planet they live in. In fact, at any given time, your body has about 10 times more foreign bacterial cells within it than its own cells (bacterial cells are much smaller than your own cells)***. And, on top of this, there is another order of magnitude of viruses that inhabit us (or our bacterial flora) for every bacterium.

***[Update: Other research suggests the number of bacterial cells within our bodies may be of the same order as our cells.]

Sometimes alien species invade our planet and (if our own immune system defenses aren’t fighting well enough) we combat them with antibiotics. However, antibiotics don’t discriminate against friendly and unfriendly bacteria, and can annihilate our friendly gut bacteria– leading to digestion issues, or even the recolonization of the gut with unfriendly species. (I’ll save fecal transplants for another post). One instance of this recolonization that has been receiving some press time recently has been of a homebrewer who had a population of Saccharomyces cerevisiae call his gut home. This single celled fungus, also known as “brewers yeast”, plagued the man by, well, doing what it does normally- metabolizing carbohydrates and producing ethanol as a waste-product. Not surprisingly, the condition is known as Auto-brewery syndrome.

Anyway, I always thought the existence of a microbiome within all of us was a really cool and astounding fact. At every instant of your life, there are hundreds of trillions of individuals living their lives within you. Awesome.

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Our message to the cosmos.

Posted on October 6, 2013 | 1 comment

In 1977 we flung an atomic powered robot into space. Voyager 1’s primary mission was to beam data back to Earth as it cruised through the outer solar system. One of the most famous bits of data sent back is this image of Earth captured as Voyager looked back towards its home planet in 1990 (Awesome commentary on this image and our planet/species by Carl Sagan here)

Pale_Blue_Dot

The Pale Blue Dot image taken 6 billion km from Earth in 1990.

 

Voyager, continuing with the momentum gained from its primary mission, has recently left our solar system and started its secondary mission of being a message in a bottle from our species to the cosmos. The message is stored on an easy-to-read golden record, and contains greetings in different languages, sounds from Earth, brainwaves of a human, and images from around the planet.

The_Sounds_of_Earth_Record_Cover_-_GPN-2000-001978

The Golden Record.

The cover of the record contains an easy to read explanation on how to retrieve the data– defining time units in the universal constant of the fundamental transition of the hydrogen atom. The location of our solar system is also printed on the cover, in relation to 14 pulsars with unique periods.

Check out President Jimmy Carter’s message to who/whatever finds Voyager- “This is a present from a small distant world, a token of our sounds, our science, our images, our music, our thoughts, and our feelings. We are attempting to survive our time so we may live into yours. We hope someday, having solved the problems we face, to join a community of galactic civilizations. This record represents our hope and our determination, and our good will in a vast and awesome universe.”

It’s awesome to know that there is a time capsule of our species and planet floating through interstellar space- likely to last billions of years in the cold reaches between the stars. I’d like the think that one day something pics it up and gets to hear Johnny B. Goode by Chuck Berry.

 

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On atoms and seconds.

Posted on September 6, 2013 | Leave a comment

There are more atoms of gold in your body than seconds that have passed since the beginning of the universe. (6.11 * 1017  vs. 4.354 * 1017 (that’s 611,000,000,000,000,000 vs. 435,400,000,000,000,000)). And what does this mean?

Well, nothing really.

I’m just trying to convey the awesome scale of the universe, both space and time, with some familiar terms. Warning: the links in the last sentence are pretty mind-blowing.

I’ll post soon on the scaling of space and time within the realm of biology, and how the space an organism takes up in space plays a role in the space an organism takes up in time (or, Lifetime vs. Body Size)

p.s. to calculate the atoms of gold from the wiki article: (2e-7 kg) * (1000 g / 1 kg) * (1 mol Au / 196.96 g) * (6.0223 atoms Au / mol Au)     (who said we would never need high school chemistry again?)

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Posted in Biology, Chemistry, Cosmology

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