oozing toward downington

Let me borrow a riff from co-blogger Allyson: Forgive me, readers, for I have slacked (from blogging, that is). It has been 50 phone calls, 200 emails, seven meetings, four gym workouts, three dinners, two "events", one screening, and a dental appointment since my last blog post. That's the downside. On the upside, it's on behalf of a good cause: getting the Science and Entertainment Exchange fully up and running. We moved into our new office this week at UCLA's California NanoSystems Institute! The phones are finally hooked up! Office supplies have been ordered (so I can soon stop borrowing scissors from the nice Korean scientist down the way)! Scientists and entertainment people are engaging in real-live interactions as I type! No doubt we'll have a few more growing pains, and there is much left to be done in terms of building out our infrastructure, assembling a nice little matchmaking database, revamping the Website, and planning special events and workshops, but I've been incredibly gratified by the welcoming attitude of Hollywood and the willingness of scientists to give of their time and expertise on behalf of a common cause.

And speaking of good causes, I'm using both my bloggy outlets this week to call attention to a fundraising effort by astrophysicists at Oxford University, selling the original photographic plates of the Palomar All-Sky Survey in the 1950s as gifts to raise money for a new antibody treatment for five-year-old Alexander Thatte -- who has been battling leukemia pretty much his entire life. This poor kid has already endured two bone marrow transplants and four years of chemotherapy; help give him one last chance at life this holiday season. (h/t: In the Dark)

So much for housekeeping. Now, I want to talk about The Blob: that classic 1958 sci-fi/horror flick -- a favorite at drive-ins back when drive-ins still existed -- where Steve McQueen made his big-screen debut as a teenager who takes his girlfriend on a quest to find out where a meteor they spotted streaking across the sky has landed. But this is no ordinary meteor: it houses an amorphous creature (the aptly named, oozing Blob) from outer space that goes on to terrorize the small town of Downingtown, Pennsylvania. It's just a small gelatinous blob at first, but then it attaches itself to the hand of one of the locals... and starts growing. And growing (as parasites are wont to do). Eventually it consumes its host completely, plus the attending ER nurse and doctor. Wackiness ensues, until McQueen's character figures out the monster's weak spot and defeats it -- at least temporarily. (There was an LA-based sequel, Beware! The Blob, that apparently was meant to be a comedy.)

The film was remade in 1988, this time with a helpful, science-y sounding explanation of where the Blob might have originated: a top-secret government experiment to create a germ-warfare weapon by isolating a virus and a bacteria (bacterium?) in outer space went horribly awry. This blogger begs to differ, offering a very convincing argument that the Blob mas more in common with the plasmodial phase of a slime mold. To wit:

"Slime molds may seem moldy, but they aren't fungi at all! They lack chitinous cell walls, have mobile stages in their life cycle, and digest food whole instead of secreting enzymes like most fungi.... Plasmodial slime molds crawl around, ingesting bacteria through absorption and digesting them intracellularly, growing and growing into a large multinucleated mass, the plasmodium..."

"The Blob's feeding habits are quite like a slime mold. Slowly crawling around, the Blob searches out food, surrounds it, and absorbs it. Slime molds do the same thing, even absorbing particles they can't digest and passing them out the other side, always hoping to engulf more bacteria. Is this any different from the Blob absorbing an entire phone booth to eat the waitress inside? .. The Blob's movement and morphology also strongly resemble that of a slime mold. Amoeboid, it branches out into many finger-like pseudopods in search of food, flowing towards its prey."

Bacteria, in contrast, are nothing like slime molds: they're tiny, they don't move around on dry land, and when they do move, it's not in any recognizable branching pattern. Nor does it make much sense for a government space experiment to combine a bacteria and a virus; as the aforementioned blogger points out, "Having a virus around would probably kill the bacteria, not mutate them into a monster, even in outer space."

The process by which cells absorb material -- usually molecules like protein -- is called endocytosis; cells engulf the molecules with their cell membrane, much like the Blob engulfs its victims (who honestly should be able to outrun an oozing amorphous pile of goo, don't you think?). I have learned some fascinating things about this biological process in the last few weeks, namely, that there is one protein molecule in particular that drives endocytosis in most cells: clathrin. It's this protein that leads to the formation of a coated pit on the inner surface of a cell's plasma membrane, which them buds into the cell -- literally pushes its way inside -- to form something called a coated vesicle. The vesicle pinches off and separates from the membrane, becoming a transport mechanism, eventually fusing with other membrane structures. This is the means by which a small volume of fluid from outside the cell gets inside... along with any other material the fluid encapsulates: cholesterol in the blood, for instance, or viruses (causing the cell to MUTATE INTO A RAVENOUS AMORPHOUS BLOB! Okay, not really... but one can get sick if enough cells are infected!).

Tomas Kirchhausen of Harvard Medical School has been studying cells' amazing ability to recycle membranes, the complex dynamics of endocytosis, and the structure of clathrin molecules, plus he's developed some pretty cool imaging techniques and animations along the way. He talked about them at October's Industrial Physics Forum (yes, I'm still combing through the rich motherlode of great science presented at that conference).

Here's some interesting tidbits. At any moment, roughly 25% of a cell's plasma membrane is made up of coated pits, each of which has a lifetime of about one minute before budding into the cell to form vesicles that pinch off and separate from the membrane. The vesicles in turn last for a few seconds, then the coat is shed,  leaving the naked transport vesicle, the coat disassembles, and the process starts all over again. But how to visualize this microscopic process in action to uncover more of the juicy dynamical details?

Kirchhausen has used a variety of methods, including spinning disk confocal microscopy, to produce real-time imaging of an "infection event" -- i.e., a virus being absorbed into a cell via endocytosis. And he used a combination of X-ray crystallography and cryo-electron microscopy to delve into the structure of clathrin and how it self-assembles into a soccer-ball shaped structure to coat a new vesicle as it forms. The individual clathrin molecule is shaped like a triskelion: a figure with three bent legs. Those triskelions assemble themselves into the soccer ball shaped clathrin coat over the course of 30-40 seconds, then they disassemble as the coat dissolves.

Here's an animated clip of the process; and here's another with actual narration. Kirchausen and his team made the movies using the 3D computer graphics/computer modeling program Maya (the Sanskrit term for "illusion," apparently), which has become something of an industry standard in TV and film -- think Pixar's Ratatouille! -- not to mention computer and video games, as well as architecture and design. It owes its popularity in part to the fact that it's designed to be open to third-party software, so users can adapt the suite into their own customized versions. (Large movie studios in particular tend to write lots of custom code for their productions.)

According to Wikipedia, Maya is, in essence, a "particle system for handling masses like steam and water drops. Dynamic fields allow adding gravity, wind and vortexes, allowing for effects such as blowing leaves, or even tornadoes. Special tools give artists the ability to brush and style particles like hair and fur." Maya comes in an unlimited version that include a fluid simulator for smoke, fire, clouds and explosions (not to mention ozzing amorphous blobs); a simulator for realistic hair (always a challenge, and still not completely realistic, frankly); and tools to simulate clothing and fabrics -- another major technical challenge in animation, along with rendering foods to look as yummy in an animation as in real life.

Rumor has it that another remake of The Blob is underway. While we're waiting to admire the wonders CGI will produce using today's cutting-edge animation techniques, take a moment to savor this little short about rendering the exquisite haute cuisine in Ratatouille. Bon appetit!