LabKitty Recommends: Partial Differential Equations for Scientists and Engineers

Back in nerd school, we did PDE out of a Well Respected (tm) brutal textbook that I will not name because who knows what roving bands of mathozoids with an axe to grind are up to these days. And it's more fun if you can guess.

Despite getting good grades both semesters, to this day I have no idea how to solve a PDE. Not even a game plan. Contrast me facing off agin' an ODE, which I also probably cannot solve but can at least get a few pokes in before it chews my arms and legs off.

Whereas ODE offer a welcome buzz, PDE are all hangover. The difference between sipping a nice Malbec by the fire and forcing down shots of homebrew teen LabKitty made using a contraption described in the yellowing pages of a Cold War era Reader's Digest found in the basement of the Circle Pines library, back when there were still libraries in a time before nomenclature was and each was all. It burned going in, burned coming out, and in between did enough chromosome damage that one temporarily qualified as a protected wetland species, genetically, before corrective nucleases had worked the necessary extra shifts to put your phenome back on the sapien branch. X-Men, indeed.

But I digress.

Motoneurons!

Happy Eigenvalue Day!

Spirobrowlf: A Free Gift for You!

Famous First Words #16: The Dawn of Resting State fMRI -- Biswal et al.

Famous First Words is a recurring LabKitty feature wherein we have a look at the opening line of a famous scientific article.

Scientists' view of the brain tends to track the popular tech of the day. Descartes, for example, knew about horses so he concluded the soul was riding the brain horse-wise and even identified an anatomical rein from which the habenula gets its name. Fast forward many years and birth of the computer got everyone certain the brain trafficked in the ones and zeros of these marvels. At various other times the brain was a state machine, or a control system, or an associative net, or a Hebbian steam engine. Who knows what models tomorrow will bring, perhaps something about dark matter or quantum foam or "rap" (I once overheard a student argue we should study the brains of "rappers" because -- and I quote -- they are the intellectuals of society.)

More to today's point, somewhere between the equine and the Boolean, psychology got enamored with operant conditioning, popularized by BF Skinner and namesake of the box that bears his name. You go in the box. You do something good and a reward (sugar pellet, whiskey, tenure) appears. You do something bad and a punishment (electrical shock, 1040, "rap") appears instead.

The effect was we came to view the brain as a passive lump existing in a kind of sensory miasma, waiting for and then responding to a never-ending parade of stimuli called life. Anyone in possession of this device might find such a description overly simplistic. If you are like LabKitty, and why wouldn't you be, your mental existence isn't a grey fog punctuated by external interruptions, but rather a rich internal tapestry of hopes, dreams, and revenge fantasies.

Git Scenarios #3: OS-X Case Sensitivity (or lack thereof)

Git Scenarios #3: OS-X Case Sensitivity

Git Scenarios is a recurring LabKitty feature wherein we examine weird / badly-documented git behaviors that may vex the git n00b (and the not-so n00b).

The OS-X filesystem is not case sensitive. That means, for example, it cannot tell the difference between a file named foobar.txt and FOOBAR.txt. You can easily verify this. Open Terminal and do:

  $ touch foobar
  $ ls foobar
  $ rm FOOBAR
  $ ls foobar

The first ls will list the file and the second will not.

Unfortunately, this can create git weirdness. Read on.

LabKitty Recommends: CORTEX: Statistics and Geometry of Neuronal Connectivity

Anatomy is the handmaid of physiology. From aardvarks to zyzzyva, if you seek to understand how something works, you must first tally its parts. Those who would take on physiology of the neural kind face a particularly uphill battle. First, brains are not built from the kind of detailed bauplan that applies to the body writ large. The shinbone may be connected to the knee-bone, but no such explicit instruction set exists for placing billions of neurons and trillions of synapses amongst them. There simply isn't enough information in the genome. Instead, we make do with statistics. Nature sketched some rules -- more what you call guidelines than actual rules -- threw us into the stew, and then washed her hands. The statistics clearly work (else you not reading this would be) but that does not mean sussing them is an easy task.

Second, even though we desire statistics writ large, it must be arduously written from the small. Neurons = tiny. You can't even see the pesky things without a microscope and even then not without preparation. Leeuwenhoek would have to wait a hundred years for the histological stains that make neurons appear in his invention, and a further hundred years for the electron microscope necessary to visualize synapses. Functional neuroanatomy is a Herculean census not of citizens but of invisible specks. No wonder protoscientists settled on the various lumps and gobbets as the fundamental units. Had you informed Descartes that it is not the pineal itself but a vast winking population of invisible animalcules within that comprise the soul you would have blown his mind.