Just a protein out for a stroll

This animation of a “walking” protein inside a cell is going viral, and I became briefly obsessed with figuring out what’s going on here. Behavior that looks conscious and deliberate can’t, of course, be deliberate or conscious at the subcellular level. It’s just as fascinating, though.

What it is: A kinesin protein hauling a vesicle (pouch that can contain various things the cell needs) along a microtubule.

How are its “feet” moving? Reactions (see video, below.)The protein floats around till one of its feet hits a microtubule, where it binds. Then that foot releases a nucleotide (ADP), which leaves a site on its surface open that gets filled by a different nucleotide (ATP); this triggers the kinesin to wave its other foot forward. The front foot attaches and starts the same cycle; the back foot processes its ATP into ADP, releasing phosphate, and detaches from the tubule, then waves forward and “takes a step,” attaching to the microtubule again.

Why does it look deliberate? The process isn’t as smooth or clean as depicted in some animations like this, which are simplified to show the essential motions. In real life, there’s more jiggling and colliding. In fact, all the floating confusion is one reason why the “two-feet” method works — the kinesin is never completely detached from the microtubule, so it doesn’t float away.

Why is it moving in a particular direction? Microtubules have polarity, and some types of motor proteins will move toward the plus-end or minus-end.

I hat-tip @picpedant, where I first saw this, and recommend this by the artist who created the animation shown above, as well as this discussion of some of the misconceptions surrounding the viral version.



This is a few months before he starts singing for the Harry James orchestra; he’s 22. The charge of sleeping with a woman is revised to adultery when she turns out to be married, and eventually dropped.

Sinatra’s life makes an interesting way to look at 20th-century America. Just this famous mugshot shows things have changed a bit since 1938: The charge is seducing a single female of good repute.

He was born in 1915 and died in 1998. Crowds screamed for him two decades before the Beatles. The documentary “Sinatra: All or Nothing at All” grounds young Sinatra in an America where race hatred commonly extended to Italians, Irish and other groups and where the Depression meant not just working hard to survive but possibly literally not surviving. Once a singing waiter, he becomes famous in every medium from radio onward; gets credited for destroying American morality by adultering with Ava Gardner; from JFK to civil rights, mobsters, Vegas and Reagan, that’s a pretty good shuffle through the decades.

He became a cliche partly because of age (paunch, fading vocals, less self-reinventing) but also by the “Seinfeld is unfunny” principle — so successful in his groundbreaking that he became the status quo. (One of my favorite moments in “High Society” is when Bing says “You must be one of the newer fellas.” Turnover is always with us.)

Late-era Sinatra parodying himself is painful, but earlier in his career, when he’s still doing it straight and singing with sincerity, the power is clear. You can probably hear it even through the audio flaws in this film of him singing to a roomful of WAVES in 1943. Criminal seduction, you say? 🙂

imageThis isn’t a Dr Pepper smoothie, of course, because the ingredients in Dr Pepper are secret, right? (See below.) But it is a quite good smoothie that soothes my Dr Pepper cravings.

  • 1 cup pomegranate-cherry juice, chilled
  • 2 cups nonfat vanilla yogurt
  • 1 cup frozen fruit — H-E-B cherry/blueberry/currant mix
  • 1 cup frozen fruit — H-E-B blackberry/blueberry/raspberry mix

(Makes about 1 pitcherful, say two 16-oz smoothies)

Internet speculation on the secret 23 flavors in Dr Pepper follows. Bear in mind it was invented in 1885:

  • Cherry, vanilla, almond, plum, blackberry, raspberry, apricot, coriander, clove, amaretto, anise, caramel, molasses, birch beer, allspice, ginger, sarsparilla, sassafras, juniper, spikenard, wintergreen, burdock, dandelion.

Glitter is sharp and bright and contains movement — like the quick trip of its two syllables set apart by sharp little t’s. One-syllable blink and wink are slow, but have movement, whether it’s your eyes or a light doing the winking and blinking (though its pace picks up when it becomes a repeated/ongoing action, doesn’t it? Winking, blinking). Gleam seems slow, soft, steady, and according to its definition applies most to reflected light, which seems right to me; my mind’s eye pictures gleaming as the yellow glow that comes off a large, smooth, golden object in a darkened room. But glow is more properly what a light source itself does; not reflecting light, like gleaming, but creating it: shine, beam, radiate.

Glimmer has movement too, but more the failure of your eyes to see something disappearing and reappearing; while its cousin shimmer has movement of a different sort, feeling more side-to-side. Or perhaps that’s shimmy I’m thinking of 🙂 (and glimpse).

Twinkle, sparkle again are repeated, sharp, two-syllable, hard consonant, flashes that repeat. Is sparkle reflected light while twinkle should be the light source itself? Nursery rhymes of stars would have it so. Flash itself is short, sharp, but without the hard consonants. Glint is quick but smaller, perhaps. Because of reflection, again? Every light loses brightness when reflected, shedding some of its brilliance as it bounces off the intervening surface. Or the moon would blind us, instead of just showing us how it sees our shared sun. Pretty flicker goes back and forth, friendly like a candle.

Scholarly side-note:

Why so many gl- beginnings in our words for light? Root words are one answer: Higueras and Clavera (2002) name two, Middle English glymsen, “to shine faintly or intermittently,” and Middle Low German glaren, “to gleam.” Sadowski (2001) compared modern English gl- root words and concluded more than half connoted light/dark or looking/seeing (with more related to smoothness, like glossy, plus glamour originally related to how something is perceived and glory also connected to light). Some scholars have even “argued the existence of sound and color patterns, whereby back vowels tend to denote dark colours (as in gloom or glum) and front vowels tend to be ‘bright’ (gleam, glitter, glimmer, etc.)” (Sadowski citing Jespersen 1922 and Jakobson 1979; front vowels being those pronounced with the tongue forward in the mouth and vice versa).

Image via Fotolia

Got a chance to crawl around inside the type of bomber my grandfather flew, a B-24 Liberator, today as several Collings Foundation aircraft visited our town. America’s most-produced plane of World War II, these heavy bombers typically dropped 5,000-pound loads of explosives deep behind enemy lines across Europe and in every theater. B-24s were harder to fly but carried heavier payloads farther and faster than the B-17. There are only two operational B-24s left in the U.S., and it was a great opportunity to look around and into this aircraft on a beautiful day. My dad and I are repairing a model B-24 and I can tell you, those distinctive oval tail fin pieces look a lot smaller in plastic.


Visitors get to step up a little ladder into the tail and go through the airplane up towards the cockpit. The B-24J would typically have had a crew of 10, including gunners at the nose, turrets, waist and tail. This particular plane is painted to represent the Witchcraft, which flew 130 missions, the most in the Mighty Eighth Air Force: http://electraforge.com/brooke/flightsims/b24_flights/witchcraftHistorical.html


Seen in the background here is Collings’ restored B-17 Flying Fortress, which we also got to see in the air a few times as it passed over.

In a 2006 CBS interview, a flight engineer from the original Witchcraft tells how he came up with and painted her nose art: http://www.cbsnews.com/news/witchcraft-flies-again-for-vets/

Climbing through the B-24 (I did get to sight and aim the waist guns):




The planes will be here Sunday as well, and visiting them costs $12 adults/$6 kids. Taking a half-hour flight in one is also possible, for $450. Till you get that saved up, here’s the video version 🙂

Here’s Robert Earl Keen as Antonio Vivaldi opening his eighth annual benefit in Kerrville for an organization he said “it’s my passion to tell people about”: the Hill Country Youth Orchestra.vivaldi crop

Keen told the crowd at the Feb. 21 show that on his travels around the country, he’ll get to talking with people about the orchestra, and they’ll say, “Oh yes, we’ve got something like that here,” and he’ll say, “No; no, you don’t.” The HCYO provides full tuition-and-fees scholarships for each of its hundred-plus students.

He’s supporting his bluegrass album “The Happy Prisoner” right now, so his part of the concert had an old-timey feel — just not as old as Vivaldi:

purple crop

But first, the kiddos cut loose with the classical goodies:

youth playing crop

(Apologies for fuzzy phone photos taken at some distance)

Watch for next year’s show, likely to be in February again, and go check it out if you can. It’s a lovely night at Kerrville’s Cailloux Theater, and this year it raised $65,000 for those scholarships. Keen closed his part of the show with a completely acoustic set, playing the special guitar they auctioned off to raise part of that money:

acoustic crop

It was beautiful.

(Fellow Aggie/Kerrville note: The auction also included Johnny Manziel autographed memorabilia. Keen is Class of ’78, Manziel is ’15)


A year kicked off with loved ones in Fort Worth is a year that’s gonna go well. I grew up near here, love the city and was tickled to hear the Metroplex referred to on the radio as “FW-D.”

Sundance Square decked out for the holidays. It was barely above freezing, so nobody’s loitering in the outdoor seats 🙂 But the restaurants and bars were doing good business and have nice views of the square!


Beautiful Bass Hall, where crowds were arriving for the New Year’s Eve concert by Robert Earl Keen:


Joe T Garcia’s turns 80 this year – the sign says “Since 1935!” Cannot count the number of great afternoons and evenings I’ve had at Joe T’s. If you go eat there on a pretty afternoon, not a freezing cold night, you can have your “family dinner” in the rambling, maze-like patio gardens out back of the old house.


First time ever to go in Billy Bob’s Texas. Bewilderingly huge and comic place, with what seemed like half of North Texas there with their New Year’s Eve dates.



But even at a distance (and this was one of the closer tables!) the Turnpike Troubadours were great. Wonderful way to ring in the year.