Friday, April 27, 2012
Day to day, I get frustrated at the pace of things: drywall mud takes too long to dry, the paint sprayer has a conniption that takes an hour and a half to fix, some shoddy carpentry that saved the builders a half hour costs me two days, and so on. But, making these problems took years. Why should fixing them take a week? At the same time, I experience a feeling that I first encountered when I published my first scientific paper: I remember reading a single short sentence, ending with "data not shown," explaining that a particular control had been performed and confirmed the expected result, and thinking, "that sentence took six weeks of hard work."
Here's some photos of one room, starting in December and ending today.
This is the room we purchased. The carpet was not in much better shape than the wallpaper.
A lot has been done, but it's hard to see. New windows have been installed--the leaky, single-paned originals swapped for double-paned, easily-moved new windows. Also, harder to see, the room has been rewired; there are two new outlets, and the existing outlet had been replaced and all properly grounded. The carpet was easy to remove; the wallpaper considerably less so.
The general consensus is that there was a square of linoleum or carpet that had been anchored down here; the floor underneath had never, ever been finished. A new light fixture has been installed to replace the kind of industrial fluorescent tubes. A two-inch hole has been drilled in the space between every stud, and cellulose insulation has been blown in. So, each hole needed to be patched with a wood plug, tape, two layers of drywall mud and one layer of finishing mud.
Skilled professionals did the sanding. The same skilled professionals did the varnishing. The only traces of this room's former ugly floor are a few hard-to-see-unless-you-know-they're-there tack holes from the carpet. The fir just glows.A drop cloth covers the now-very-expensive floor. The holes in the wall are patched; they've been painted over with a primer with grit in it to match the texture of the original lath-and-plaster walls. A great deal of caulk has been applied (such is life with 80-year-old plaster; even the tiniest crack benefits from some flexy caulk). The ceiling has been primed and painted (Benjamin Moore "Calming Cream"). The windows and trim have been masked, and the walls primed and painted with two coats (PPG "Sorbete de Melone")--enough to hide the original pukey color.
The walls are all masked so that all the trim can be painted. It takes two coats of primer and two coats of paint (Benjamin Moore "Antiquity") to hide the hideous pink and green.
All the trim has been painted, and where the masking tape either leaked or tore off the existing paint, the touching-up has been finished. There is still more to do--paint the switch and plug plates, paint and install the 1/4 round of wood that goes between the baseboard and the floor, paint and hang the doors, install shelving in the closet--not to mention furnish the thing. But, it's still useful to step back and look at how far we've come. GAAAAGH! CHANGE IT BACK! NOW!!!!
The weather, on the other hand, has been more equivocal. There were a couple of sunny days in the 80's, but there has been at least one shower, sometimes very heavy, every other day for the last couple of weeks.
*I really wanted to post a picture of a shooting star that the Real Doctor found--but the next day was one of those in the 80's, and the poor thing melted.
Monday, April 23, 2012
Saturday, April 21, 2012
The previous shower/tub had the pipes coming out of the floor on the window side of the room. We re-routed them to the other side, and put them in the wall. Rather than metal pipes, we have PEX plastic, which is totally dope. One other thing--see how high that shower head is? Yay! No more stooping in the shower!
The bathtub got installed pretty early in the process. We chose this model for a couple of reasons...First, it fit; second, it had a reasonable step-over height and reasonable depth, a high overflow drain, and a nice flat rim--so, a good soaker if need be. This model is acrylic; the runner-up was iron, which (given our floors) kind of scared us.
With tub and plumbing in place, it was time to put in the drywall...
...and put up the walls of the shower.
The walls are "LivingStone" (TM)(R)(Copyright). Installing them was a bit of art. None of the walls are flat, so it wasn't a matter of just cutting out a rectangle and slapping it in place. The contractor had to make a precise template (he used strips of veneer and hot glue) and cut each piece to spec; you can see the shims he used to get the right space for the silicone sealer, and the corner blocks for holding the corner joints just so. The horizontal band is waiting to be filled...
Continuing with the walls, we wanted some bead-board wainscoting; to get that to fit, I had to do the same business with cutting templates--only a bit more so, since I had lots of plumbing to work around, and (since the walls were 80 year old plaster rather than nice new sheet-rock) they were skewy and screwy, with no right angles anywhere. Also, I ended up using cardboard for my templates, which didn't work as well (lesson learned).With the bead-board cut, the problem was how to attach it to the wall. Liquid nails is the solution, but then the problem is how to press the board up against the wall while the adhesive dries. The solution there is go-bars: giant springs made of wood, pushing against the opposite surface:Next: What's a bathroom without a toilet? And what about the golf balls?
Tuesday, April 17, 2012
This month, Tennessee enacted a law that would require education officials at the state and local level to
assist teachers to find effective ways to present the science curriculum as it addresses scientific controversies…[and] help students understand, analyze, critique, and review in an objective manner the scientific strengths and scientific weaknesses of existing scientific theories [such as] biological evolution, the chemical origins of life, global warming, and human cloning.
These “teach the controversy” laws are a nod and a wink to creationists and global warming deniers, denizens of that parallel world I visited earlier. Meanwhile, in the reality-based community, we have some really fun studies that engage real questions about evolution.
One of the long-standing tussles in evolutionary theory is about what pushes evolutionary change. In one corner we have the adaptationists: folks such as Richard Dawkins (and many microbiologists) who see good old-fashioned Darwinian natural selection as being the main force behind change. In the other corner we have the stochasticists: folks who argue that chance fluctuations and genetic drift in small populations are the main way that changes get established within a population (the blog Sandwalk is an example; to some degree, Stephen Jay Gould was of this school).
Evolutionary biologists of both stripes have long known that islands are prolific incubators of unique species. The Galapagos Islands are the classic example, but pretty much any island chain will have its oddities. My favorites are California’s Channel Islands, with the world’s second cutest fox species and the oxymoronic pygmy mammoth. Adaptationists will say that the unique, isolated environment of any island will drive evolution of founder species in idiosyncratic directions, producing species perfectly and uniquely adapted to every specific island. Stochasticists will say that island species are typically “founded” by a very small number of individuals, and since no individual perfectly represents a species, the differences between island species are due to these “founder effects.”
If you were a god, the question of who is correct here would be easy to solve—simply find some islands with distinctive (but related) species, and reverse time’s arrow until you arrived at the common ancestor of all the different types. Being merely human, though, you could do what a group of researchers from Harvard, Duke, and UC Davis did, and act like a god to a bunch of lizards.
When I was a kid, I was a god to a lizard; it was a Carolina Anole that we bought at the Los Angeles County Fair, where it was sold as a “chameleon” because of the species’ ability to change color from muddy brown to green. Anoles are native to the islands of the Caribbean, where, over millions of years and hundreds of islands, they have diverged into many different species. Why so many different species? Are the individual islands all so different that they select for unique adaptations, or are we seeing the effects of chance events in small populations?
To play god for these lizards, the researchers took advantage of an "act of god". A hurricane had eliminated the lizard population of seven tiny islands in the Bahamas. The researchers repopulated each of these lizard-free islands with an anole Adam and Eve, chosen at random from a large and well-established population on a nearby island.
For the stochasticists, this is a promising start. Given that each island’s Adam and Eve were randomly chosen, some of the islands would start with larger-than-normal founders, and others would start with smaller-than-normal founders. Stochasticists would believe that subsequent generations would bear the signatures of their founders, and that you could tell many generations later whether an island’s population had been founded by a relatively large or small Adam and Eve.
What about the adaptationists? The godlike researchers had something to satisfy them as well. It’s pretty well established that small shrubs—like those found on the new islands—provide a selective advantage to anoles with shorter limbs. The Adams and Eves chosen to populate these islands came from a population that had evolved with big trees, and so tended to have long limbs. Thus, all the new populations were subject to selection pressure to make their limbs shorter with every generation. Adaptationists would believe that, after a few generations, all the anoles on all the islands would have the same short limbs, regardless of which Adam and Eve founded their island’s population.
Part of being godlike is being patient, so the researchers gathered data on these lizards for four years; the populations of the islands grew from their founding couples to thirty or forty lizards, all of whom were subject to annual measurements of limb length and other characteristics. All the lizards also gave DNA samples to be sequenced, giving the researchers a certain godlike omniscience about these beasties.
So, after four years, what did the researchers find? Were the stochasticists right, and the lizards descended from larger Adams and Eves remain larger? Or, were the adaptationists right, and all the lizards got smaller and smaller limbs?
Of course, as one of my teachers would say, absolutists are always wrong! After four years, all the lizard populations had clearly evolved by selection. On every island, the population’s limbs were all shorter than the limbs of that island’s Adam and Eve. However, after four years, the imprint of the founders was still visible—the larger the founding couple’s limbs, the larger their descendents’ limbs. In one potent, information-packed graph, we have this result about the last years of the study:
(The islands have poetic names like "N1" and "N15"; all populations evolved towards shorter limbs, and generally speaking, larger-limbed founders lead to larger-limbed descendants. Just to be sure, the researchers followed the large population that provided each island’s Adam and Eve, and it barely changed over this time.)
There’s two other things that the lizard gods noticed in their study. One thing fit in very nicely with the stochasticists’ world-view. The researchers measured the amount of variation in some of the lizards’ DNA sequences (they looked specifically at non-coding DNA, a sort of filler that is not essential or even useful to the lizard; all animals have lots of this, and by definition it is not affected by selection, only by stochastic events). In the generations of Adam and Eve and their first offspring, the lizards on each island had a lot of variation in their DNA sequences. However, in succeeding generations, this sequence variation collapsed. The populations experienced a genetic bottleneck, and all the subsequent generations showed the effect—essentially, they became highly inbred. This fits with the stochasticist view of how island populations evolve and become different from one another, as each population’s genetic variation collapses around a different focus.
Another observation bolsters the adaptationist viewpoint. Most of the lizard populations peaked after three or four generations, and were actually in a significant decline as the study ended. This is a phenomenon that would be unsurprising to the Rev. Thomas Malthus: a small population in a rich environment expands, and eventually exceeds carrying capacity, leading to a crash. Under such circumstances, the selection pressure gets turned up to eleven.
The authors of this paper are not godlike enough to see into the future. Really, they studied just the very beginning of the island evolution process, and nothing like speciation has happened yet. The authors suggest that the adaptationist trend will dominate in the short term (especially given the pressure of overcrowding), driving all the populations to a similar conformation. However, beyond that they are agnostic: there aren’t any significant environmental differences between the islands (at least, any that they can perceive), so selection will no longer work as a force to make the island’s populations divergent. Also, the islands’ populations are really small, so it’s relatively easy for a chance event to have a profound effect. Retreating from the role of omnipotent and omniscient gods, they assume the mantle of Solomon, and judge the case of stochasticist v adaptationist by cutting the baby in half.
Kolbe, Jason J., Manuel Leal, Thomas W. Schoener, David A. Spiller, and Jonathan B. Losos (2012). Founder Effects Persist Despite Adaptive Differentiation: A Field Experiment with Lizards. Science 355: 1086-1089.
Monday, April 16, 2012
Opal genuinely liked to be on the bench with me when I played the piano. She was not especially prone to singing along; she just liked being near. It seemed to calm her down, and no matter how agitated the music, she would chill out.
She was also capable of trenchant musical criticism. Years ago, I was learning Beethoven's "Waldstein" sonata, a monument of the piano repertoire. It took me a long time to learn each movement, and then put them all together. The first time I played the whole thing all the way through, when I finished, I looked down at her, she looked up at me, and then she barfed on the piano bench.
Sunday, April 15, 2012
Having gutted the 'loo and made it structurally sound, it was time to start filling it in. A lot of things went on at once, but I'll try to take things in a more orderly manner, starting with the ground up.
We are currently renting a house in Roseburg, and it's a pretty nice place. The bathroom is nothing special, but it does have one nice (if completely accidental) feature. There is an exhaust pipe for the water heater and central heat located in the basement crawl-space beneath the right-hand-front corner of the sink. It takes the sting out of waking up on a cold morning to stand on this one particular tile as you do your morning ablutions.
It turns out you can achieve this effect intentionally, so the Real Doctor and I decided to splurge and get a heated floor for the bathroom. Although it's an electrical heater, it did create some friction--it's not clear whether its installation falls under the purview of the tile guy or the electrician. Eventually, they played along. The tile guy arranged the heater wires on the floor and taped them down, and the electrician fed them through the conduit into the wall outlet:
Next, the tile guy laid down a layer of cement. This was one of those things that really required some art. Our house is old, and there is no surface, floor, wall, or ceiling, that is truly flat or perpendicular to any other. However, a bathtub needs to be flat (that is, with reference to the earth's gravitational field, not with reference to any nearby wall or floor) to drain properly. So, the tile guy had the unenviable job of getting the floor to tilt and warp and skew so that it joined together all the walls, the tub, and the door without resembling a Pringle. Impossible to see in this photo, but it took some significant time and skill.
The tile we chose is a marble subway tile; rather than putting in each tile individually, they come glued to square-foot sheets of mesh. There's still a lot of cutting and trimming that needed to be done to get everything to fit well, requiring skills and tools that I don't have. The edge is made from doorway sills:
And finally, some grout. We opted for an epoxy-based grout that is supposed to be extremely easy to clean and mold resistant--we'll see how it works.
Of course, first thing we did was try out the floor heater. It takes a while to heat up--but it's got a thermostat with a programmable timer, so you can set it to be warm when you wake up in the morning. It feels divine.
(We aren't at this level of decadence yet, but I have heard of heated toilet seats. As a 5-year old, I lived in New Zealand for a year. I remember that it was quite cold in the mornings, and the best way to start the morning was to be the second person in our family of five to use the loo. The first person got the most immediate satisfaction of biological urges, but the second one did pretty well in that regard and got a warm seat.)
Saturday, April 14, 2012
Color # 1
The choices are "Squish-squash," "Lion Heart," "Sorbete de Melon," and "Ticul." Which is which?
You may choose which is which with a roll of the dice, but it was a lot more painstaking for us to arrive at our decisions. The local paint store has a color consultant, who would come out with her decks of color cards for PPG and Benjy Moore, and we'd pore over these. Then, we'd get samples--sometimes the store has little trial jars, sometimes we'd have to get a specially brewed pint or two--and try them out.The process is baffling--the same color looks completely different on different walls and in different light. As always, it could be worse: the paint store's record is a person who tried seventy-two different specially blended colors of paint (and this was at a time when the smallest paint sample was a quart!). You put the stuff up on your walls in the full awareness that you have no idea how it will turn out.
And, of course, as this view from our driveway shows, nature is only too happy to show that we are pikers at this color-blending game.
Wednesday, April 11, 2012
Monday, April 9, 2012
The death panel met repeatedly during the last week, without really getting convinced one way or the other about the best course of action for its charge. Sure, the patient was old and had many conditions, any one of which could be painfully terminal within a year. However, as the panel was meeting, the subject demonstrated a renewed, hearty appetite and actually ran during her daily walks. The subject of the panel's debate was our 13-year-old Pomeranian, Opal, a dog internationally famous for her page-turning skills.
The last two nights, Opal weighed with her own view on the debate. From about midnight 'til about 4 AM, she affirmed that it was time to go. Not "time to go" in the way that a dog complaining in the middle of the night means it. Time to go in the way meant by a dog suffering, uncomprehendingly, from kidney stones and renal problems. Lots of narcotics were given, but they took a long time to calm the agitated panting and restlessness, and left Opal kind of foozy and sore the following day. Not the way for a dog to be. The gall bladder that was supposed to be operated on turned into the least of her worries.
So, today, we took Opal to a friend/vet at her farm, where she was given a dose of muscle relaxant and sedative. After resisting it, twitching like she was falling asleep, she became calm in my arms--calm like she had not been in weeks. She was given a shot of a fatal cocktail, and within minutes her breathing and pulse coasted to a halt. She now lies beneath the big oak tree at our new farm, and will become part of the sod.
Opal was a really sweet, charmingly weird, nice dog. I'm sad, of course, but I know that she had a pretty good and long life, she gave us wonderful memories that will make us laugh and cry years from now, and we gave her with what I hope was the best death possible. What more can be hoped for in any life? Requiescat in pace, and may her memory be for a blessing.
Saturday, April 7, 2012
Four or five glasses of wine**, lots of myth, and a full moon will have their effect:
*Or as brother E. calls it, "it's that holiday with the parsley, isn't it?"
The full moon looks down on me
Walking my dog after too much dinner.
The same moon looked down
When my Grandaddy fled the Ukraine;
The same moon looked down
When Israel fled the Pharaoh.
Once again, despite the full feast,
I’ll want to be elsewhere next year.
Once again, despite the efforts of the good,
Shalom is a stranger in Jerusalem.
Once again, despite the extra setting,
I suspect Elijah will not be joining us...
I can’t know this for sure.
So I set the prophet a place and pour him some wine,
I try to do good and fix the world,
I try to be a student of Moses and Hillel,
And whether it’s a place on Earth or just in my heart,
I’ll say, “Next year in Jerusalem.”
**Manischewitz--the only Kosher wine available in Roseburg. Yeeeeeeeeecchhhhh.
The bathroom we bought was of a piece with the rest of the house: good bones, especially considering when it was built, but kind of run down and wanting repair.
So, that's a claw-foot tub, some pretty marginal shower hardware, a pretty crappy crapper (not shown--the plumbing, which was pretty bad) and a sink that was OK but at the very least needed re-finishing. The floor is fir, but it's really worn and the varnish has died and so the wood is getting damaged. The walls are papered with blue paper that was kind of dark and peeling. However, it was nice and compact and flooded with light from an outsize window. The layout was fine and the built-in medicine cabinet has design features that make it harmonize perfectly with the rest of the house.
So. We decided to keep the basic outline, update all the plumbing, wiring, lighting, and fixtures, and add just a few touches to make it perfect. It's close enough to done now to write about.
Step one was to find fixtures. Most modern bathrooms are the size of bedrooms, it seems--two sinks, a shower and a huge tub, commode, cable TV, bar...they are getting out of hand, and fixture design has kept pace; much of what is sold today is simply too big to fit in our 'loo. So, we had to troop up to Eugene to do some shopping. Fixtures in hand, it was time to get to work.
Step two was to clear everything. The claw-foot tub weighed a ton--it's pretty much a lump of cast iron. Right now it's sitting on our front porch, but we've sold it to a couple who live further out in the country. They want to put it on their deck and make it into a "hillbilly hot-tub." More power to them! That's probably better than the traditional use of old tubs in the Real Doctor's native land. The custom there is to put it in the garden, tipped up to form a protective grotto for a statue of the Blessed Virgin Mary or JC. The toilet and sink are going to a recycler who sells such things to people who want antique-y stuff for their renovations.Unsurprisingly, the sub-flooring was just as toasted as the flooring--extensively water damaged, so most of it had to go too.
Even less surprisingly, the plumbing was awful. The pipes were mostly cast-iron/rust in a 50-50 blend. The access port for the sewer line from the toilet had broken off, leaving it permanently open in the basement. Probably for the best that we don't have any pictures of that, or what the basement was like underneath that.
Neither the Real Doctor nor I am wild about claw-foot tubs, so we decided we would install a real shower stall with a real shower head that was taller than me. This meant ripping out a lot of lath-and-plaster, and finding some of the things that were in the walls. This is one of several multi-generational mouse nests we found.
After installing PEX or PVC plumbing for everything, we could put in a new subfloor; it was nice to walk in there without sinking down ever so slightly.
One unfortunate thing about having a proper shower stall instead of a claw-foot was that the big ol' window had to be shrunk. In order to keep as much window as possible, we decided to shift the remaining bit window over to the right as far as possible. So, take out the existing window:
Frame in a new one:
Put in a nice, double-paned, reeded-glass window and some drywall:
And, trim the original wooden framing to size and slip it on. There ya go!
Up next--fixtures and finishing! Oooooh, the excitement!
Friday, April 6, 2012
Monday, April 2, 2012
Absent anything presentable, I will quote this, which circulated 'round the intertubes a couple of weeks ago. If you haven't seen it, you should. It's from Czech dissident/jazz musician/etc Josef Skvorecky, describing the instructions given to pop bands by the Nazis after they took control of Czechoslovakia (full article here, worth reading):
- Pieces in foxtrot rhythm (so-called swing) are not to exceed 20% of the repertoires of light orchestras and dance bands;
- in this so-called jazz type repertoire, preference is to be given to compositions in a major key and to lyrics expressing joy in life rather than Jewishly gloomy lyrics;
- As to tempo, preference is also to be given to brisk compositions over slow ones so-called blues); however, the pace must not exceed a certain degree of allegro, commensurate with the Aryan sense of discipline and moderation. On no account will Negroid excesses in tempo (so-called hot jazz) or in solo performances (so-called breaks) be tolerated;
- so-called jazz compositions may contain at most 10% syncopation; the remainder must consist of a natural legato movement devoid of the hysterical rhythmic reverses characteristic of the barbarian races and conductive to dark instincts alien to the German people (so-called riffs);
- strictly prohibited is the use of instruments alien to the German spirit (so-called cowbells, flexatone, brushes, etc.) as well as all mutes which turn the noble sound of wind and brass instruments into a Jewish-Freemasonic yowl (so-called wa-wa, hat, etc.);
- also prohibited are so-called drum breaks longer than half a bar in four-quarter beat (except in stylized military marches);
- the double bass must be played solely with the bow in so-called jazz compositions;
- plucking of the strings is prohibited, since it is damaging to the instrument and detrimental to Aryan musicality; if a so-called pizzicato effect is absolutely desirable for the character of the composition, strict care must be taken lest the string be allowed to patter on the sordine, which is henceforth forbidden;
- musicians are likewise forbidden to make vocal improvisations (so-called scat);
- all light orchestras and dance bands are advised to restrict the use of saxophones of all keys and to substitute for them the violin-cello, the viola or possibly a suitable folk instrument.
(I sometimes play too strictly; I had a teacher who would urge me to squelch my inner German.)
Sunday, April 1, 2012
Bacteria have an endless ability to amaze. Even plain old Escherichia coli, the workhorse organism of thousands of labs—an organism that, in my youth, I thought too boring and well-known to be worth focusing a career on—still generates research that leaves us dumbstruck and groping for explanations. Nowadays, as often as not, these surprises turn up on the fringes of science and don’t really affect our understanding of how the world works. However, they do make us pause and scratch our heads—sometimes at the result itself, other times at why the initial experiments were done. So, we have findings from Czech researchers about how E. coli in “heavy” water (enriched for the deuterium isotope of hydrogen, 2H2O) grow faster than they do in normal water. We have the finding from an astrobiology group that growth in zero gravity causes changes in the expression of almost half of E. coli’s genes. And now, a new report suggests that E. coli can actually sense and respond to sound—in a word, bacteria can hear.
The finding, like many in the history of science, is an example of Pasteur’s dictum about fortune favoring the prepared mind. In this case, the mind belongs to Felix Balatro of Miskatonic University. He was actually testing a pet hypothesis about whether Bacteria could learn.
Of course, one would not expect terribly deep thinking from a bacterium. Nor would you expect deep thinking from the flatworm Planaria—however, this has been demonstrated using a T-maze. A T-maze is the simplest possible maze: the worm can go forward from the bottom of the T to the top, then it can turn left or right. If the reward is consistently on the right, then the little guys start turning right more than half of the time. Balatro had the rather crazy idea that bacteria could do the same trick. One problem he had to solve was a matter of scale: a planarial T-maze is a few centimeters long, a distance that would take a couple of generations for E. coli to swim. Fortunately, advances in microfluidics and techniques borrowed from semiconductor production enabled him to produce a T-maze of millimeter scale, with exactly equal concentrations of an attractant (aspartate) at each branch of the maze.
Now, the first piece of luck for Balatro was that he didn’t really think this through. Planaria, being flatworms, have a clearly defined left and right. They crawl, instead of swimming. So, the right side of the T-maze corresponds only to the right side of the flatworm’s body. Not so with E. coli. They swim, and spiral and loop and frequently tumble as they swim, so they “know not their right hand from their left.” Anyone knowing this basic fact of E. coli’s biology knows that this experiment would fail—but Balatro, either through ignorance or (more likely) stubbornness, pushed ahead.
Amazingly, E. coli seemed to learn to turn right. Balatro ran his cells through the T-maze, and collected the cells that made it to the right side of the maze. Using some nifty microfluidic devices, he let these cells reproduce for one generation, and ran them through the maze again. Again he selected the cells that turned right, and let them grow again…and again, and again, for approximately a thousand generations. After this time, when he ran a thousand cells through the maze, he found that between 60 and 70% of the cells would turn right.
This result is completely, totally, 100% unbelievable. Being a good scientist, Balatro didn’t believe it. Suspecting some barely perceptible turbulence in his test chamber, he turned the microfluidic slide upside down in the microscope—and obtained the same result. He wondered if the bacteria were somehow responding to light, so he blacked out his lab and ran the cells through the maze with the microscope’s lights out—and again found that nearly three quarters of the cells turned right.
Magnetotaxis—the ability to sense and respond to the Earth’s magnetic field—is not unknown among the bacteria, so Balatro tried to test this. “Right” in his original maze corresponded to south-southeast. He spent a day rearranging the tangle of pumps and controllers surrounding the apparatus so that “right” now corresponded to north-northwest, and he must have experienced a mixture of surprise and elation when he found that now, 75% of his cells got to the T and turned left!
Balatro’s celebratory mood was presumably deflated when he shared his results with his colleague, D. Avril Poisson. She looked through the microscope at the maze, coolly removed a magnet from a nearby refrigerator door, and set it upon the stage. The resulting magnetic field was many times stronger than the Earth’s, and the bacteria did not change their behavior at all. In fact, when Balatro ran the experiment in her presence, the bacteria seemed to forget everything—they got to the T, and half turned left, half turned right.
Here’ was Balatro’s second piece of luck. It had to do with a combination of his intellect and his personal eccentricities. I got to know one of Balatro’s PhD committee members when I was in graduate school, and she described him as “one of the most brilliant and…um…uh…ehhh…I guess you could say lateral thinkers I’ve met.” He apparently lived in the lab, only going home to shower; he spent a fair amount of his time in lab stoned, and he spent absolutely all of his time in lab, awake or asleep, with the stereo blasting the Grateful Dead at deafening volume. He even ditched one thesis advisor (and, thus one field of study and one future career) for another solely because his newly chosen advisor was deaf and didn’t mind the noise—and so oncology’s loss was microbiology’s gain.
Rather than mope about a failed experiment, Balatro realized that only one thing had changed when Poisson had entered the room. Out of hard-learned politeness, he had muted Jerry Garcia’s solo from “Sugaree” at the Rockpalast, 1977, blasting from the speakers in the south end of his lab. Nothing else had changed—nothing about light, the magnetic field, temperature, pH, nutrient or redox gradients, or any of the myriad other things bacteria are known to sense. Just pure, Gratefully Dead sound. Had he discovered phonotaxis?
Of course, Balatro confirmed this result, and spent a lot of time designing experiments that eliminated other possibilities and left the conclusion that his bacteria could hear and turn towards sound. And so we have the paper, given the innocuous title “Novel functions for mechanosensitive channel proteins in an evolved Escherichia coli system,” and slipped into print in the obscure journal Acta Pathologica, Microbiologica et Immunologica Scandinavica. It’s as if Balatro doesn’t want us to notice that he has discovered something incredible.
However, this is a powerful paper; Balatro, working with Poisson, even proposes a plausible mechanism. Sound, at the cellular level, is a mechanical phenomenon—an alternation of high and low pressure. Bacterial cells have mechanosensory proteins in their membranes, and these have been intensively studied for their role in helping cells survive osmotic stresses. These proteins, as they sit in the cell’s membrane, are deformed when the cell membrane is deformed; the change in the protein’s shape causes the protein to send a signal into the cell, resulting in a change in the expression of several genes.
Balatro and Poisson examined the genes for these mechanosensory proteins, mscL and mscS, in the cells that consistently turn towards high-intensity sound, and found that these genes had evolved over the course of generations of selection. The genes had, in fact, recombined with genes for chemotaxis—that is, genes that encoded proteins that sensed food, and directed cells to swim towards higher concentrations of food. The evolved gene encoded a hybrid protein that still sensed mechanical pressure (though this too had changed slightly), but now controlled the cell’s swimming behavior.
This result is curious, and leaves open lots of questions. We still don’t quite understand how sound waves, which should be much larger than a bacterial cell, can have a perceived direction to E. coli—it would be as if we could tell, just using our own senses, what direction a change in barometric pressure came from. There is also the puzzle of how the changes in the pressure-sensing component of the MscL and MscS proteins in these “hearing” bacteria relate to their ability to hear. Information about the structure of these mutant proteins should provide some answers, and Balatro is quite able to get that data rapidly.
Ultimately, like cells growing in Deuterium or microgravity, this is a completely artificial situation, and thus not likely to be of especial biological significance. Still, it’s pretty neat, and a good reminder of both how science progresses and how amazingly extraordinary even “ordinary” bacteria can be.
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