Culturing Science – biology as relevant to us earthly beings

RSS link update

Hey guys,

The RSS feed guys over at Sciam took the day off so our links were broken AND wrong. D’oh!

Here’s the correct RSS feed link! Update your feeds, people.

Thanks to all who sent me kind words throughout the day. I’m reenergized and ready to take back what’s mine — i.e. the internet.



Written by Hanner

July 6, 2011 at 12:14 am

Posted in News

Culturing Science is moving… to Scientific American!

Hello Friends,

I’m pleased to announce that Culturing Science has a new home — the brand spanking new Scientific American blog network! It’s a lovely group with many of my favorite science bloggers and you can find us all in the same place.

What does this mean for CS? Not much. I will post more because I am contractually obligated, but also because I am now a part of this wonderful community and I want to engage with them. I’m going to finish up zombie blogging, continue the history of science series, maybe even finish up some even older projects that I never got around to.

Read my intro post here, and check out the other blogs here. Bora Zivkovic has a great post introducing all the blogs.

Switch over your RSS feeds here!

I am thrilled and hope you’ll join me at Sciam.



Written by Hanner

July 5, 2011 at 7:36 am

Posted in News

3Quarks Daily Science Blogging Contest: Vote for someone!

Why write again what Jason has already written?

Why write again what Bora has already written?

“The great science blog 3 Quarks Daily has announced the voting for it’s third annual prize for the best science writing on blogs. Last year, the judge was Richard Dawkins. This year, once the voting by the public narrows down the choices, the finalists will be judged by Lisa Randall.

Check out the nominees and then vote for your favorite.”

So this year, several of my posts were nominated. Vote for one of mine, or vote for another, but definitely vote.

Voting closes Wednesday at 11:59pm eastern time (8:59pm pacific time), so do it soon!

I’ve got 1 million friends who were nominated for their great work. Just vote for SOMEONE, alright? If you vote for me you get a high-five!!

I’ll be back to blogging again soon. Between a fabulous weekend of blogging for the World Science Festival and starting my internship at Nature Medicine last week, I’ve been a bit swamped. But see you soon – ON THE INTERNET.

Written by Hanner

June 7, 2011 at 12:05 pm

I have not abandoned you.

Making promises, breaking promises.  Zombie biology week is on standby — but for good reason! I have had lovely friends flying from around the country to stay with me over the past couple weeks (and the coming weekend). As much as I was tempted to tell them, “thanks for flying out here, but … I have to blog, so see ya later,” I resisted. (Just kidding, friends, I lurve you.)

My promises will be kept — they’re just on hiatus. Zombie biology, classical science, and a couple other ideas rumbling around in this little brain of mine will come to fruition, just not this month.

In the meantime, to get your Culturing Science fix, I have some ideas.

First, the 3Quarks Daily Science Blogging contest is open for nominations! The contest, honoring the “best writing in a blog or e-zine in the category of Science” with $$$ prizes, is judged by theoretical particle physicist and cosmologist Lisa Randall and any blog post written after May 22, 2010 can be nominated! All you have to do is paste the URL of the post into the comments here. A sentence of praise or two is welcome but not required.

So why not relive the memories, friends — here are some of my favorite posts from the past year (in chronological order) and, if you find them worthy, you can nominate me! Only one nomination per person so be sure to check out my blogroll and other blogs to make sure you’re making the best choice. Nominations close May 31, 2011.

If that’s not enough for you, I do writing places besides here… at The Scientist! Here’s some recent stuff I’ve written for them. I’m finding my mind expanded by being forced to write about disease, cancer, molecules … but more on that later.

That’s enough self-promotion for one day. See you next month!

Written by Hanner

May 25, 2011 at 3:38 pm

Posted in My life

The Biology of Zombies

Night of the Living Dead (1968)

I am that girl who is the least fun to watch movies with (or the most fun, I guess, depending on your idea of fun). I love science fiction and respect artists and writers who alter the science of our world to tell stories — but I’m still going to want to have that talk at the end that starts with, “But it wasn’t actually that realistic when…”

For about a year now I’ve been interested in doing some writing about the biology of zombies. They’re ubiquitous in modern culture and stories tend to take a half-assed shot at the science, as if they feel they need to provide a mechanism for the spread of flesh-craving, but they can’t quite figure out how to make it work.

So when Krystal D’Costa of the fabulous blog Anthropology in Practice brought up Zombie Awareness Month last week on twitter, I couldn’t help but throw some ideas out there. And when she suggested that we do some organized zombie blogging, I couldn’t resist. She has a great post up about the anthropology of zombies — check it out here!

And then when I got down to research … I had so much that I wanted to say that one post was not going to be nearly enough. So get ready for a fun-filled week of zombie science!

What I’m mostly interested is the science fiction aspect of it — not trying to make up my own theory for how zombies could actually exist (though that is obviously part of the fun of this analysis!), but rather exploring the theories of different stories. I’m going to write about several causes of zombie-ism (bacteria, chemicals and viruses) focusing on a particular work or two, plus a day for zombie neuroscience and one for zombies in nature. I’ll update this post with links as the week goes on.

I’d love to hear your thoughts, especially comparisons to other books/movies/television, since I have not come close to exhausting the possibilities.

Don’t forget to visit Anthropology in Practice to learn about the public fascination with zombies.

 Other zombie science resources (to be updated all week chronologically so tell me about yours!)

  • “The zombiesm bacterial story is central to Left 4 Dead — the first person shooter” (tweet from Troy Christiensen, @ShalimarTroy)
  • The Strain — “The vampirism in that book is caused by a virus carried by parasitic worms” (tweet from Matt Henry, @greenideas)
  • James Byrne of Disease Prone has two great posts up: The first contemplating whether zombies are technically alive and the second enumerating zombies in nature
  • Zombie Neuroscience expert (seriously) Bradley Voytek answers a question on Quora: What are some ways to survive the zombie apocalypse?
  • Bradley has also given a talk about zombie science at Nerd Nite San Francisco which is posted on his blog along with some lovely words about why he cares about zombie neuroscience

Written by Hanner

May 17, 2011 at 12:53 pm

Zombie Biology, Pt. 2: Zombie neuroscience

This is the second post in a 5-part series on the biology of zombies. More info and links to other posts here.

Zombies in The Walking Dead

When I watched the first episode of The Walking Dead series, based on the comic book series of the same name, I was stunned: “They can show this on TV?!” Apparently we now live in a society where it’s ok to show a horse being disemboweled, with a mere warning of graphic imagery at the beginning of the episode. Some of my friends thought the plot dragged on through the first season a bit, but I loved it.

And one of the show’s most endearing details to me was that the safe haven city (supposedly) was Atlanta, Georgia. Not because I think it’s a great city or anything, but because this choice showed the emphasis the writers put on science: Atlanta was the city worth protecting because it is where the headquarters of the Center of Disease Control (CDC) are located. After all, if anyone is going to cure a zombie outbreak, you’ve gotta protect your scientists!

The zombie virus spreads into the brain in The Walking Dead

After surviving countless horrors, Rick and his small posse of survivors finally make it to the CDC, expecting to find a city of scientists working swiftly to find a cure for zombie-ism who would take them in. But when they go inside, they find a single man — the last man standing, working alone towards a cure in the vast complex.

Because no mad scientist is able to hold in his secrets, he quickly gives in and explains to them what he knows of the science behind the zombie outbreak. He asks his computer to call up TS-19: A video of the electrical impulses in the brain of Test Subject 19, a volunteer who allowed the scientists to study her as she succumbed to her zombie bite. As they watch the neuron’s of the still-human brain flicker on the screen before them, Dr. Jenner explains:

Somewhere in all that organic wiring, all those ripples of light, is you — the thing that makes you unique and human… Those are synapses, electric impulses in the brain that carry all the messages. They determine everything a person says, does, or thinks from the moment of birth to the moment of death.

The survivors gaze slack-jawed at the light show before them until the brightness begins to dim, with black roots growing up from the base of the neck into the brain, until everything goes black. “What is that?” they ask. Luckily, they have a SCIENTIST in the room!

It invades the brain like meningitis: the adrenal glands hemorrhage, the brain goes into shutdown, then the major organs — then death. Everything you ever were or ever will be, gone.

But wait, there’s more. After a little while, between 3 minutes and 8 hours, according to Dr. Jenner, the black roots turn to a glowing red, reactivating just the brain stem. (I’ll give the writers the benefit of the doubt and say the scientists recolored the zombie electricity later for effect.)

It basically gets them up and moving… [but] it’s nothing like before… Dark, lifeless, dead. The frontal lobes, the neocortex, the human part — that doesn’t come back. The you part.

While a nice shot, this explanation wasn’t satisfying enough for me. Sure, the brain stem might get em moving, but what makes a zombie want to eat other people? What makes them murderous, and angry?

I’m fortunate that I didn’t have to do this research because it would take far too many hours to get me competent in brain territory. But Dr. Steven Schlozman of Harvard Medical School made a fabulous video going through each aspect of zombie behavior and explaining what parts of the brain must be reactivated for a zombie to really exist! (via bioephemera)

But there is another zombie-related brain question — why do they want to eat human brains? BRAAAAAIIINS?

This never made sense to me. I mean, after a while, when the zombies gather in hordes and there are few living humans around, you would think they would need any energy they can get and not really discriminate by species or favored body part. Of course, not all zombies eat brains — in The Walking Dead they’ll eat anything, animals included, and the entire thing. (So resourceful.)

Perhaps brain-eating rose as a zombie characteristic because if they ate all of their victim, zombie-ism wouldn’t propagate very far. Gotta leave the prey a leg or two so that they can stumble and limp appropriately and, since zombies are altered in behavior, maybe they’re missing part of their brain. Got it.

Creepy zombie torso explains why she craves brains

Perhaps my favorite zombie movie is Return of the Living Dead, featuring punks fighting zombies (with a great soundtrack to boot). According to Wikipedia, this is also the film that debuted the zombies craving brains, with their stereotypical yell: “BRAAAIAIIINNNS!”

While hiding out in a funeral home, the humans manage to capture a decaying zombie torso — which I believe is given a tribute in the first episode of the Walking Dead (see how I did that? full circle!) — and they tie her up and ask her about her habits. “Why do you eat brains?” She told them that it helps her to cope with the pain of being dead. “I can feel myself rotting… [Brain] makes the pain go away.”

It’s unclear how exactly this helps — what is it about brains that would dull the pain of feeling your own body rot? But at least it’s an explanation, and, being as obnoxious as I am, for me any explanation in science fiction is better than none.

Zombie biology, Pt. 1: Richard Matheson’s bacterial symbiosis

This is the first post in a 5-part series on the biology of zombies. More info and links to other posts here.

A little girl zombie eats her victim in Night of the Living Dead

The rise of the zombie in pop culture is typically credited to George Romero’s ghouls from his Night of the Living Dead films, whose dead bodies reanimated with a taste for human flesh define our prototypical zombie. Romero doesn’t give a clear cause for their rise from the grave, with a vague mention in a television broadcast of a satellite returned to Earth from Venus emitting radiation. (Radiation could do anything back then!)

In a behind-the-scenes special about the making of the movie, Romero credits its creation to a short story he had written, “which I basically had ripped off from a Richard Matheson novel called I Am Legend” —  a great horror story about Robert Neville, a man fighting for his life in Los Angeles against vampires. But the novel takes the vampire prototype and turns it on its head, with these creatures more recognizable as zombies to us than vampires. They aren’t the sneaky serial-killer types, but are rather stupid and gather in great hordes, and, like zombies, will feed upon one another if they must. (Yes, they have blood!) In an early chapter, Neville reads Bram Stoker’s novel Dracula (as he sips whiskey and listens to Brahms while vampires scream outside his house), describing it as “a hodgepodge of superstitions and soap-opera clichés” compared to his situation at the time.

Most of the standard vampire tropes hold true: they’re sharp-toothed, blood-sucking, repelled by crosses and garlic, and can’t come out in the sunlight. But this is science fiction — there must be a scientific cause for these symptoms! While he’s skeptical of the scientists’ germ theory of vampirism that was proposed before the scientists became vampires themselves, Neville eventually overcomes his “reactionary stubbornness” and gets a microscope. (And Matheson doesn’t leave out the difficulties of microscopy or mounting samples, with Neville throwing his first scope across the room in frustration.)

When he finally gets his slide loaded with a sample of vampiric blood, he is shocked to see a bacterium in the sample — a bacillus, “a tiny rod of protoplasm that moved itself through the blood by means of tiny threads that projected from the cell envelope.” And from there much of the book turns to scientific inquiry with many moments that made me smile, like when Neville so urgently “needs to know!” that he nearly runs out of the house into a vampire horde. Oh, the drive of science! Or when he can’t make the pieces fit into his bacterial model and begins to work himself up into a fury:

He made himself sit down. Trembling and rigid, he sat there and blanked his mind until calm took over. Good Lord, he thought finally, what’s the matter with me? I get an idea, and when it doesn’t explain everything in the first minute, I panic. I must be going crazy.

But over the course of years, performing experiments on captured vampires and their blood samples, as well as doing a lot of hard thinking, Neville manages to explain to himself why the vampires act the way they do. Whether his explanations will be good enough for you is another question.

The bacterial lifecycle

Bacteria from the same genus as Neville -- this is Bacillus subtilis, while he found Bacillus vampiris

“I dub thee vampiris,” he says to himself when he sees the bacteria for the first time. The bacteria live in the bloodstream of their host and require fresh blood to live, living in a kind of symbiosis (described thus by Neville), with the bacteria generating energy for their hosts. But if there isn’t enough fresh blood around, a bacterium will sporulate, building a cell wall around itself to hide out until better conditions arise. When the host dies, these spores disperse, landing on a new host, with the new source of fresh blood reviving the vampiris bacterium.

In the novel, the bacteria were able to spread rapidly through the population due to dust storms, with the wind blowing the spores everywhere and the dust nicking peoples’ skin and thus creating a way into the body.

Neville’s discussion of bacteriophages is a moment of total scientific inaccuracy which I choose to ignore. His bacteriophages, which he describes as proteins that the bacteria secrete when conditions are poor, cause the bacteria to swell and explode, killing themselves along with the hosts’ cells. The thinking must have been that the bacteria need a way to kill their hosts so that their brethren spores can disperse — however a bacteriophage is not a protein, but rather a virus that infects bacteria.

Death by stake — an issue of bacterial metabolism

These vampiris bacteria can live with or without oxygen — aerobic or anaerobic metabolisms. In the bloodstream, they live without oxygen, but the second oxygen hits the system, they become parasitic, killing their host. And here’s where the stake comes in: The key to killing these vampires is creating a hole large enough to let oxygen into the bloodstream, causing the host to die immediately due a switch in bacterial metabolism. And when the host dies, the spores are released — and thus we have vampires exploding into dust. Once Neville realizes that it’s an issue of oxygen and not stakes or their material, he switches his method to simply slitting the wrists of the vampires to let oxygen in. “When I think of all the time I used to spend making stakes!” he says.

And why don’t bullets kill vampires? This is some embarrassing fabricated “science:” The bacteria cause the creation of a “powerful body glue” that seals bullet holes as soon as they are formed. (Though this body glue somehow can’t reseal the wrist slits.) The stake creates a large hole and blocks the body glue from resealing it, which is why they are such a potent weapon against vampires.

Other bacteria-based vampire symptoms

Philip Burne-Jones's painting The Vampire (turn of the 20th century)

Neville read that strong sunlight kills bacteria, which is why vampires can’t go out in sunlight. But without fresh blood, the bacteria can’t create energy — resulting in the coma-like state of the vampires during the day.

One of his first experiments is trying to work out the vampires’ aversion to garlic. After reading that garlic’s potent odor is caused by allyl sulfide, he goes to a chemistry lab and heats mustard oil and potassium sulphide at 100 degrees to create the compound. First he tried injecting it into a vampire — but nothing happened. He expected the bacteria to be killed by the allyl sulfide in a lab experiment, yet again nothing happened! He was so infuriated by this failure of his theory that he downed a bottle of whiskey, broke a bunch of glass, and shredded a mural he painted.

World’s gone to hell. No germs, no science. World’s fallen to the supernatural, it’s a supernatural world. Harper’s Bizarre and Saturday Evening Ghost and Ghoul Housekeeping. ‘Young Dr. Jekyll’ and ‘Dracula’s Other Wife’ and ‘Death Can Be Beautiful’. ‘Don’t be half- staked’ and Smith Brothers’ Coffin Drops.

He stayed drunk for two days and planned on staying drunk till the end of time or the world’s whisky supply, whichever came first.

Yup. Just a normal day in the lab.

He later realized that this chemical in the bloodstream wasn’t enough. It was the actual odor of the garlic that did harm — an allergen that sensitized and repelled the bacteria, and hence their hosts. Tells you something about in vitro and in vivo experiments, am I right?

“The germ also causes, I might add, the growth of the canine teeth,” he mentions once near the end of the novel. Good save, Matheson.

Vampire psychology

Neville wasn’t satisfied by this theory alone — what about the mirrors and crosses?

A new approach now. Before, he had stubbornly persisted in attributing all vampire phenomena to the germ. If certain of these phenomena did not fit in with the bacilli, he felt inclined to judge their cause as superstition. True, he’d vaguely considered psychological explanations, but he’d never really given much credence to such a possibility. Now, released at last from unyielding preconceptions, he did.

Before society collapsed entirely when vampirism was spreading, in terror people turned to religion to calm their fears — The vampires were cursed by god for their sins, and only by accepting god could you be saved! Neville theorized that when these people, now convinced that evil people were condemned to vampirism, were infected by the bacteria and found that they themselves were vampires, they were driven mad. The mere sight of the cross — a symbol of their rejection — made them want to flee due to their self-hatred.

But the cross doesn’t apply to everyone, he noted. He had one Jewish friend that, as a vampire, was not repelled by the cross. But the sight of the Torah made him run in fright!

Mirrors had a similar effect. Having to actually face the fact that they were vampires visually was enough to drive them nuts and induce them to flee.

Ending teaser (but not a spoiler!)

There are a few other awesome biological references in the novel — including the lymphatic system, medical applications and evolution, which I won’t go into detail about here so you can enjoy the read. But I will tease with this quote, especially appreciating that this book was written in 1954.

He looked into the eyepiece for a long time. Yes, he knew. And the admission of what he saw changed his entire world. How stupid and ineffective he felt for never having foreseen it! Especially after reading the phrase a hundred, a thousand times. But then he ’d never really appreciated it. Such a short phrase it was, but meaning so much.

Bacteria can mutate.

Bacterial vampirism: it’s awesome!

I’m no expert, but this was the only example of vampirism being caused by bacteria that I could find. This novel certainly inspired many later stories of plague-based apocalypse and biological transmission of zombie-ism, but, after a few decades of focusing on radioactivity and biological warfare, the genre switched straight to viruses (to be discussed later this week) and never went the bacterial track.

But there’s plenty of good reason to consider bacteria and other spore-based organisms when developing your zombie mythology, especially since there are a number of examples in nature (also to be discussed later). It’s an underexploited transmission mechanism! Get on it, filmmakers.

And one final note — I Am Legend is really awesome and you should read it. Trust me — there is MUCH to enjoy despite what you’ve read here. This is really a novel about human loneliness, perseverance, and our definition of normalcy, after all.

Lazy Sunday Video: A tour de force through the history of life

Posting the lazy sunday video at 4pm: That means it’s an exceptionally lazy day!

But it’s also an exceptional video — one of my favorites that I’ve seen on the whole of the internet. (Gasp!) Piecing together clips from dozens of science documentaries and specials overlaid with stunning music, the youtube user UppruniTegundanna starts out tracing the history of humans, integrating technological and artistic development. Then it takes a turn to beautifully visualize the most severe mass extinctions on this planet before starting from the beginning — from the big bang, formation of the solar system and earth, the first molecules and the evolution of life as we know it.

It’s a lot of ground to cover and it’s so well done. Get ready for 12 straight minutes of butterflies and chills. I haven’t failed to get them each time I watch it, an unquantifiable number of times at this point.

In this video and his others, the artist seems to truly grasp the magnificence of the universe. At its heart, this video is about natural disasters, embracing extinction and death as key to how we got here. In a lovely blog post this week, Patrick Clarkin wrote:

Eugenie Scott, Director of the National Center for Science Education, has written that for many laypeople the notion that evolution is an unguided, mechanistic process implies that “life has no meaning.” However, contrast that view with how many scientists write about nature. The sense of awe and reverence that is exuded is palpable.

And this video exemplifies this — true awe at the fact that we exist at all.

Written by Hanner

May 15, 2011 at 3:24 pm

Erasistratus on the nature of scientific inquiry

I am thankful for many things in my life and one of those is that, still in high school, I discovered not only one but two intellectual passions. One, as you know, is biology and the other is Latin and classical history. I struggled a bit in college because I felt like I was split in two, spending half of my time in classes for each, and never able to wholly invest myself in the study of either. I simply couldn’t choose and the two fields felt mutually exclusive — after all, what could be more different than analyzing ancient texts that many argue are dead in our time and working to understand concepts at the fringe of modern discovery?

But that all changed when I read Lucretius for the first time. In De Rerum Natura he explained and beautifully illustrated with words the Epicurean doctrine, bringing me to tears at times. And at the heart of that philosophy is the atom — and when I read that word (he uses “primordium,” the origin or beginning, or “seminarerum,” literally the seeds of things) my world changed. I had found an overlap — the study of classical science! While I wasn’t able to take any other classes on the topic, the idea didn’t stray far.

While Aristotle gets a lot of attention, his work is typically slated as philosophy rather than science. Not only does he have many works on natural history, but there are many other classical scientists that we only have a few scraps of, or are referenced by later authors with no source material to look back on. But many of the works of these early scientists and philosophers are gems in which we can see the reflection of the early days of  modern scientific inquiry — both in the things they got right and, more frequently, the things they got wrong.

Now I’m finding that, if I decide to go back to school, this is what I want to study. I have these books — so why not start exploring the idea further on my blog? So, yes, I will. Welcome to Classical Science on Culturing Science.

I’m going to start off with a lovely quote from Erasistratus of Ceos (or Erasistratos of Keos) who wrote around 280 BCE about the nature of scientific inquiry — and it sounds more than a bit familiar. None of his writings are extant, but he was quoted by the medical researcher and philosopher Galen, who lived in the 100s CE.

Those who are completely unused to inquiry are, in their first attempts, blinded and dazed in their understanding and straightway leave off the inquiry from mental fatigue, and are no less incapable than those who enter races without being used to them. But the man who is used to inquiry tries every opening and he conducts his search and turns in every direction and so far from giving up the inquiry in the space of a day, does not cease his search throughout his life. Directing his attention to one idea after another that is germane to what is being investigated, he presses on until he arrives at his goal.

I don’t think that requires any commentary.

For this project, I will be ever indebted to the work of Georgia Irby-Massie and Paul Keyser who put together a sourcebook of Greek science. The above translation is quoted in their book from G.E.R. Lloyd’s Greek Science after Aristotle. At some point I do plan on throwing my own translations into the mix (only Latin, obviously) — get pumped!

Lazy Sunday Video: Endangered species vs. humans

Balancing the needs of endangered species that can damage human property and the people that own the property is quite the trick — one that hasn’t exactly been figured out yet. Ranchers call the conservationists arrogant hippies, conservationists call the ranchers heartless and selfish.

And as with so many of the battles in our species, it all comes down to property — who has right to the land? I think it’s a particularly interesting facet of the right-to-property debate because it really is so easy to understand where each side is coming from, especially as an outsider, while such squabbles (or wars) within our own species get complicated very quickly.

This short video by Jeffrey Mittelstadt, a UNC master’s student in documentary journalism, does a great job articulating the argument between the two “sides” by interviewing a rancher and a government worker working to protect the Florida Panther. You can read an interview with him as well.

Hat tip to Jason Goldman

Written by Hanner

May 8, 2011 at 11:50 am