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.

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.

LabKitty Recommends: Mathematics of Epidemics on Networks -- Kiss et al.

All cultures need a foundational document. A kind of explanation of the world cum moral compass. Comfort for when the night is dark and full of terrors but the cable is out so HBO can't distract you with Carice van Houten's magnificent boobies. Something to shelter inside while you are sheltering inside.

But what? we reasonably ask. Christians have the Bible, Republicans have Machiavelli's Prince, barnyard animals have The Art of the Deal. What selection is available for the average punter trying to make sense of current events?

LabKitty recommends Mathematics of Epidemics on Networks. Not a phrase I ever expected to write, what with having experienced an actual epidemic on a network, but I think you browlf the context.

LabKitty Recommends: Don't Make Me Think -- Steve Krug

The reason most academic websites are horrid even though they were made by smart people comes down to one issue: user experience. If you've ever attempted to navigate, say, GitHub or OpenNeuro, it's easy to tell usability was an afterthought. Why wouldn't it be? After all, if you're an expert in SVC or MRI or Bayesian diffeomorphic wavelets, how hard can designing an interface be? It's just a bunch of buttons, right?

Wrong.

Don't Make Me Think (now in its 3rd edition) is a classic on Web usability. In it, UX guru Steve Krug tackles the causes of and cures for bad design. The unifying theme is the book's title, but Krug breaks this down into easily digestible chunks: homepage etiquette, navigation consistency, tips for clear page layout, helpful versus unhelpful text, search box dos and don'ts, accessibility, and -- most important of all -- how to test the usability of your site. Examples are scattered throughout, with bad before and better after screenshots demonstrating how the book's ideas are put into practice. His focus here is commercial websites, but Krug's advice is pertinent for any application.

The book's style is breezy and clocks in at around 200 pages, making it an easy weekend read. So for the love of Cats, if you're planning on turning something loose on the general public -- especially something the rest of us will be forced to use -- please please please read Krug's book first. You no longer have any excuse not to.

PS: Krug's guidelines also apply to academic software (looking at you, Connectome Workbench).

Start improving your product with Don't Make Me Think on Amazon.

LabKitty Recommends: A Git Book

LabKitty Recommends is a recurring feature wherein I recommend something.

Linus Torvalds is the George Lucas of computing: He had one good idea a long time ago, and now nobody dare raise a hand to his awful ones. Case in point: git and its daemon spawn GitHub. In a righteous world, they would have done to Torvalds' career what "Rock me Tonight" did to Billy Squire's. Instead, nerds wet their knickers just typing the names, all-the-while pretending that perfectly good SVC solutions didn't exist long before git's fresh hell was loosed upon the world. Apparently we'll suffer any sling and arrow for a chance to sit at the cool kids' table. Software development is just high school with different bullies.

Infamous for horribleness, git is also the rare topic for which Internet help is useless. The contraption's forced popularity has ironically killed Google as a resource. Any git-related search will return a virtual mountain of answers. Half of these will be clickbait. Half of the other half will be from people only interested in demonstrating how much smarter they are than you. Half of the third half will be wrong, and at least one of the answers is guaranteed to destroy your work.

Sure, somewhere buried in this Zeno partition may be what you need. But if you could finger the correct answer, you wouldn't need help in the first place.

What to do?

LabKitty Recommends: Principles of Brain Evolution -- Georg Striedter

Things are they way they are because they got that way. A remarkably simple idea that explains the complexity of the world. Of course it's true. You need only break open the nearest vertebrate and count cranial nerves to be convinced. And it's a far more satisfying explanation than my Circle Pines VBS could muster, not to mention the shrill shrieking daughters who regularly prowl campus with their mini-wheat bibles railing against the evils of academics, what with our discovering longer-lasting lightbulbs and cures for diseases and whatnot. Say what you will about Darwinists, at least they never bombed a church or flew an airplane into a skyscraper to impress their god.

Still, there are many gaps to fill when considering how we went from amino acids to Shakespeare. This keeps bookstores and libraries well-stocked with evolution titles of every stripe and spot. Alas, I find most of these to be insufferable. Case in point: On the Origin of Species. I've tried to read OtOoS. I really have. It's pretty much required if you want to be taken seriously by the inhaler-and-pocket-protector crowd. But, like the Principia, I just couldn't power through it. The latter because I didn't purchase a Newton-to-reality decoder ring, and Darwin's epic because I couldn't stay awake. How can something so wondrous be made so dull? Beak lengths? Seriously, dude? Darwin could crush the fun out of going to the Moulin Rouge on two-fer night. He's like Malthus for people who find Malthus too randy.

But use cyprinid vagal lobe cytoarchitecture to argue lamination emerged repeatedly during speciation because it's an efficient synaptic geometry and you got a stew goin' baby. So I was muy pleased to recently come across Georg Striedter's (UC Davis) romp through my wheelhouse. In his Principles of Brain Evolution, he sets out to establish, well, principles of brain evolution. How that information processing porkchop in your noggin came to be. How is it different from other brains? What makes mammals special among the vertebrates, primates special among mammals, and humans special among primates?

LabKitty Recommends: Stats Data and Models -- Richard De Veaux et al.

In one of his biographies, Richard Feynman recounts the tale of being contacted by a civilian seeking advice on how to join the rarefied members-only club of the physicist. Where does one begin? the man asked. What should he study first? Is it best to start with differential equations? Ordinary or partial or stochastic? What about Lie algebra or algebraic topology? Or perhaps group theory or measure theory or number theory?

Feynman replied the true path to physics was none of those. Instead, he recommended the man simply think about the things he sees every day. Why are the colors of a rainbow in the order they are? Why does touching the bare ends of a wire together make sparks? Why does a magnet attract iron but not aluminum? Why is the sky blue? That, more than any mathematics, is what physics is really about (Feynman conveniently overlooking the infinite dimensional Banach space path integrals he used to snag a Nobel. But I digress).

I was reminded of this anecdote after recently stumbling across a copy of Stats: Data and Models. For I have spent many dark nights grappling with the statistics equivalent of path integrals in infinite dimensional Banach space -- sometimes successfully, sometimes not. Richard De Veaux and his coauthors provided me my own personal Ratatouille moment. A return to the simple roots of statistics, before it became a freak show of covariate matrices and Markovian bootstraps and what all else.

LabKitty Recommends: Augustus -- The Life of Rome's First Emperor

History doesn't repeat but it rhymes, I think R.F. Laird said. And with America days away from inaugurating a reality TV star as president, surely we have turned some corner toward the collapse all empires eventually suffer. Why not read up on how we have arrived at this crossroads? As I have argued in these very pages, it was Octavian who got the ball rolling, tipping an ethereal line of dominoes that has been clacking down through the ages, dividing the world between a competent before and an incompetent after, a crazy train headed for the cliff with no brakes and no doors on which we all currently ride.

Sickly, prudish, lucky, politically savvy, militarily inept, a hard worker, a devoted husband, and a genuinely nice guy when he wasn't butchering political opponents (including family members). Also: very rich. This is the portrait Anthony Everitt paints of Augustus in his slim biography. The image called to mind is Don Corleone played by Enid Strict.

Even then there are surprises.

LabKitty Recommends: Neuroanatomy To Color and Study

Harper/Perennial publishes a series of coloring books on technical topics that provide a creative way to learn complex material. Having a student actively participate in the presentation promotes retention. Such pedagogy is routinely applied in the classroom, but H/P's use of interactive content in print was innovative. A co-opting of the familiar childhood pastime, albeit the subject matter detailed and mature (perhaps "graphic textbook" might be a better descriptor than "coloring book").

Many of the series offerings are in anatomy. The flagship is arguably The Human Brain Coloring Book, assembled by neuroscientists Marian Diamond, Arnold Scheibel, and Lawrence Elson and illustrated by Cinthea Vadala and Janice Aspelin Schwegler. These are respected names in the field. (Diamond published the first study of Einstein's brain. What made Einstein smart? Short answer: We don't know. Longer answer: Go here.) More to the point, anatomy has always been a visual subject and THBCB continues a tradition we can follow back to Leonardo's parchments and Galen's sand drawings.

But it's not what I came here today to recommend.

LabKitty Recommends: A Second Course in Elementary Differential Equations

LabKitty Recommends is a recurring feature in which I recommend something.

An inescapable obstacle in learning mathematics is its trade off between allure and difficulty. I do not know, nor can I recall, how public school math teachers sustain a veneer of enthusiasm for the piffle which appears thoughout the agoge. What's that? Why is the quadratic formula important? Well, children, you use it when you're enclosing a fenced area in a square! And, um, maybe to balance your checkbook? Have I mentioned enclosing a fenced area?

It is the very definition of a no-win situation. The truth may set you free, but here the truth would cause students to riot and may well get you fired. You really want to know why the quadratic formula is useful? All right, here's the truth: It's not. There. I said it. All the happy cartoons in the world showing everyone from astronauts to zoo keepers using the quadratic formula in their daily life won't change that. It's a stepping stone. A way-station. If you understood contour integration we might be able to converse about something interesting. But noooo, NCLB says that's too "advanced" for third grade.

Here our harsh mistress smiles in a manner indistinguishable from a sneer. Suffer the little children.

LabKitty Recommends: Quantum Mechanics in Simple Matrix Form -- Thomas Jordan

LabKitty Recommends is a recurring feature in which I recommend something.

Two households, both alike in dignity, in fair Germany, where we lay our scene. The star-crossed lovers in this version of the story are Erwin Schrödinger and Werner Heisenberg, who independently develop two versions of quantum mechanics. However, in contrast to the many times in science where two people make the same discovery, Schrödinger's and Heisenberg's theories look completely different. Schrödinger based his theory on a partial differential equation; Heisenberg based his on matrix algebra. The quantum virtuoso Paul Dirac would later prove the two approaches were equivalent, but for a few turbulent years in the early 1920s Schrödinger and Heisenberg battled for the hearts and minds of the physics community, each expecting to be greeted as liberator.

Predictably, what with differential equations being complicated and hard and matrix algebra being straightforward and easy, physics embraced Schrödinger's approach and threw Heisenberg to the wolves.

Seriously.

LabKitty Recommends: Fundamental Neuroscience -- Duane Haines (ed.)

Pop quiz: What do neuroscience textbooks and samurai movies have in common? Answer: The giants in the field tend to overshadow the little guys. Kurosawa's oeuvre all but eclipses the films of other directors working in the samurai genre, such as Yoji Yamada's quiet and wonderful Twilight Samurai or Takeshi Kitano's 2003 remake of Zatoichi. In neuroscience, aspiring authors must contend with the monster tag team of Kandel's Principles of Neural Science in one corner and Parent's (nee Carpenter's) Human Neuroanatomy in the other. One is reminded of T.S. Elliot's quip that Dante and Shakespeare divide the world between them, there is no third.

Many people like Kandel (the book not the guy, whom I assume many people also like). I had a two-semester survey course out of it in grad school. My neuroanatomy prof didn't use Carpenter -- she felt the level of detail was unnecessary -- although I wish she had. The writing is oddly compelling for what is, let's face it, a dictionary of brain parts. However, Principles left me cold. We could look into why that is and what it says about me, or we could move on with life and check out what does get my fur puffy.

Which brings us to Fundamental Neuroscience.

LabKitty Recommends: The Trilobite Book

Riccardo Levi-Setti has been writing books on trilobites for decades, but none more sumptuous than his latest. If your idea of these extinct arthropods is grey lumpen shapes dotting some nondescript rock outcropping at the local museum, then let The Trilobite Book absolve you of that notion. Levi-Setti gives us a coffee table collection of exemplary finds from around the world -- North America to Russia, Newfoundland to Morocco

There are no nondescript lumpen shapes here. We see trilobites preserved forever in defensive posture (all for naught, obvs), in mid-molt, or assembled in a mass gathering (probably in preparation for egg fertilization). Digital colorization of the images brings out important trilo-details, although many specimens exhibit brilliant colors in situ (yellow or red ochre if FeO2 or FeO3 was deposited during fossilization. Or, on rarer occasions, calcium carbonate, which renders the fossil chalk white. Ghost trilobite!). And those details are astonishing. Ogle cranidial furrows and librigena, tuberculated carapaces and pygidial spines, flowing cephalic processes and waving eye stalks. Indeed, an entire chapter is devoted to the trilobite's famous schizochoral eye -- individual ommatida organized into a logarithmic spiral, separated by a sclera and protected by an overhanging eyeshade that functioned as a primitive pupil -- the superb preparations producing anatomy that is eerily lifelike.

Large-eyed mummy of ancient rocks, Timothy Conrad penned in his Ode to the Trilobite in 1840. Levi-Setti gives us a visual experience of these mummies returned to life, a glimpse of Ordovician seas hundreds of millions of years before the first human arrived on the scene.

See Trilobites on Amazon

LabKitty Recommends: Science Ink

The days when only dangerous folks have tattoos are waning, membership in the Yakuza or Hell's Angels no longer a prerequisite to "get ink done" as the Offspring say. So why not scientists? We're not typically dangerous individually, what with our slight torsos and little garter snake arms, although we do remain dangerous in the abstract. Just about everything ever invented, from calculus to 5-axis NC, was immediately put to use devising more efficient ways to kill each other. Heck, most scientists have things in their lab freezer that could wipe out the Eastern seaboard. Not that any of us would. Just, you know, don't make us angry.

Enter Carl Zimmer's Science Ink: Tattoos of the Science Obsessed. A coffee table book with lots and lots of glossy photos of kindred spirits sporting various science-themed tattoos both iconic and obscure. Each entry comes with a bio blurb of the subject and a review of the relevant background. Equations, molecules, and trilobites are popular, but all of the major topics get a chapter -- math, physics, chemistry, astronomy, earth sciences, evolution, neuroscience, with some hard-to-classify works collected in the final chapters "nomenclature" and "what the mind makes." The artistry on display ranges from humble to holy freakin' cow, the latter category including some spectacular protein structural models and a number of Darwin arm sleeves. Should you have any lingering prudish misgivings, I assure you the poses are all modest in the extreme. Nothing you need keep hidden from the kids. More Mary Curie than Kat Von D.

So if you've ever wondered what our esteemed scientists are wearing under those lab coats as they ponder and titrate, Carl Zimmer has your answer. If 300 could get teenagers interested in reading Herodotus, who knows what some buff kitty sporting a Schrodinger's equation across their attractive parts might do for our nation's sagging SAT scores.

See Science Ink on Amazon

LabKitty Recommends: Introduction to Probability Models

LabKitty Recommends is a recurring feature wherein I hit you with a book that struck my fancy. Easy to find on Amazon, yes, but your local independent bookseller also appreciates your patronage. Do with this information what you will.

When I was a LabKitten, I took karate lessons at a local strip mall. This in an attempt to ward off the Nelson Muntzes and Scut Farcuses of the world. All for naught it turned out, and a CCP makes the whole enterprise rather moot. Still, the instructors were quite good, especially for a strip mall dojo. They took their job seriously. It certainly wasn't Cobra Kai, but scrapes and bruises and bloody noses weren't uncommon.

I had a favorite instructor, who for the sake of discussion I shall call Doug because that was his name. Doug was the nicest guy you'd ever want to meet. He was also a genuine badass. I forget what degree black belt he was, but I remember watching the black belt tests. At that level, the school would bring in the head honcho from overseas and he would decide what the test would be. It seemed to me the test was always something like "the last person not unconscious, passes."

Doug was a fantastic teacher -- patient, attentive, skilled in getting a point across. He genuinely wanted his students to progress. But he was terrifying to spar against. He would line up in front of you and the friendly instructor you thought you knew would vanish. Instead, some impostor with dead eyes would take you out for a ride. I felt like Paul Atredes sparring with Gurney Halleck, thinking his beloved mentor had sold out to the Harkonnens and was trying to kill him. Looking back, I understand now Doug was teaching us about facing a situation where you are unquestionably going to lose. What are you going to do about it?

LabKitty Recommends: BUGS in Writing

The quickest way to ensure the writing on your blog will be riddled with mistakes is to recommend a writing book. (Is that ironic? Ever since the whole Alanis Morissette debacle, I'm never sure.) LabKitty has dared such hubris before, with Karen Gordon's Transitive Vampire and Matt Young's Technical Writer's Handbook being featured here in previous posts. I don't make such recommendations as presumed expert, but rather as struggling artist. Trapped in the grammar gutter and looking at the stars, as it were. A literary Fur Club for cats.

Yes, I am a serial em-dash abuser and a junkie for inappropriate British spelling. That and which are my bête noire, I can't keep straight when you have to spell out numbers, and I have given up entirely on lay and lie. I am only now figuring out proper parenthetical punctuation, I place commas to make a sentence read like it hear it in my head, and Kurt Vonnegut will get my semicolons when he pries them from my cold dead prose. All this is mostly a nonissue in my professional nerd writing. Journal publishers and tech pubs departments both provide a grammar safety net, albeit one leading to tense email exchanges explaining, yes, the punctuation should go outside the quotation marks because typing the grammatically-correct version of the command would erase the hard drive, and, yes, "albeit" is a perfectly good word. Alas, Blogger doesn't offer the luxury of $100 page charges and a bevy of English majors who humiliate you at the company volleyball outings, so here we are.

LabKitty Recommends: Amusing Ourselves to Death

Stop hurting America.

With those three words, Jon Stewart knocked Crossfire off the air. It was glorious to behold. Not quite "tear down this wall" or "have you no sense of decency," but still. Those of us who lived through the dark times thought Tucker Carlson's reign of terror would never end. We pinched ourselves, not believing it was really over (I follow the Moskva, down to Gahrky pahrk...).

Crossfire had become a symbol of everything that is wrong with television journalism. Public relations masquerading as public interest, where corporate interests and their advertising dollars get softball questions and a free pass. They made the fatal mistake of bringing Stewart on the program. A Trojan Rabbit. Stewart went off script. In the tradition of the court jester, he spoke truth to power. The rest is history.

The show would eventually recover, but Carlson would not. Crossfire slinked back onto the air after an eight year hiatus with new hosts. Carlson was last seen on Fox News begging for change and ranting about Vince Foster. Maybe he and Matt Drudge can form a ventriloquist act where one drinks a glass of water while the other tells Monica Lewinsky jokes. Which one is the dummy? They both are.

Jon Stewart. Carrier of the Gleaming Sword of Truth.

Well, maybe not.

Have a seat, because I have some bad news.

LabKitty Recommends: Prime Mover -- A Natural History of Muscle

Steven Vogel is the Stephen Jay Gould of biophysics; what Gould did in bringing evolution to the masses, Vogel does for physics applied to living things. He has given us books like (the award-winning) Cat's Paws and Catapults, Vital Circuits: On Pump, Pipes, and the Workings of the Circulatory System, and many others. Eminently accessible treatments explaining the manifestations of Newton's laws, fluid mechanics, and thermodynamics at work inside each of us, be you cat or some other lesser creature.

For my money though, his best work is Prime Mover: A Natural History of Muscle. Here, Vogel takes a look at all things muscle. How it works and how we found out. How we exploit mechanical advantage in everything from hand tools to sports to killing. The upper limits on exertion. Why humans are (probably) good to eat. Why we suck at flying. Vogel presents not just the what and how, but also the larger implications on history and culture. The anthropology of biophysics, so to speak. Why a horse is a better choice than an ox for a farmer (and why an elephant isn't). Why East African women carry heavy loads on their heads and not on their backs. Why George Washington considered arming his soldiers with the bow-and-arrow instead of muskets. And if you ever find your party stranded in the Alps or on an elevator, the chapter Muscle as Meat will help you decide who (and what) gets eaten first.

If you're looking for an adventure that features not only sarcomeres and hemoglobin but also an analysis of the Greek trireme and a history of the prison treadmill system, Prime Mover is just the ticket.

See Prime Mover on Amazon

LabKitty Recommends: The Illustrated History of Europe

LabKitty Recommends is a recurring feature wherein I hit you with a book that struck my fancy. You can look though all my recommendations by clicking on the appropriate Blerg link over in the margin.

The challenge of understanding history isn't the details, it's getting the big picture. Consider Herodotus, who invented the discipline with his massive volume on the Persian Wars. Such a fixation of focus is with us to this very day, as can be verified by a cursory glance at the history section of your local bookstore. Rows and rows of ginormous tomes, each addressing a single topic. The Boxer Rebellion. The presidency of William Taft. The use of Tupperware in the Sutton Hoo ship burial (ok, I made up that one). The point being is if you wish to soar hawk-like over the great stage where humans have played out their little foibles rather than scrutinizing the individual planks in the rostrum you are mostly relegated to books with titles like "Hey, Dummy..." or "An Illiterate's guide to...". What to do?

Enter The Illustrated History of Europe. Barnes and Noble Books sat down eight experts on different eras of European history, gave them a big pot of Frappuccino, and commanded them to dish. Frederic Delouche then applied Adobe Illustrator and a stern backhand and edited their contributions into a glorious telling of Europe, all the way from the Romans up to the formation of the EU. Chocked-full of facts, bursting with artwork, and (wait for it) out of print. What the heck, universe??

The Illustrated History of Europe can be purchased from used book sellers everywhere (whom you should patronize this and every holiday season, if only to stave off the coming dark age for as long as possible). If you can't tell Augustus from Augustulus, or the 30 years war from the 100, or if you only know Napoleon as ice cream, here is your first inroad to the big picture of history.

Check it out on Amazon

LabKitty Recommends: Core Text of Neuroanatomy

Learning anatomy is about as much fun as memorizing multiplication tables. So why is Carpenter's textbook so darn readable? It's like a crisply-written novel, with plot fleshed out in characters of nuclei, fiber tracts, gyri, and fossa. I should note this is the pared-down "essentials" version -- the unabridged edition of Carpenter is about twice as thick (and is now authored by Andre Parent as Carpenter has passed away). What's left out? Who cares! Whether you forgot all the stuff you memorized from Parent or I forgot all the stuff I memorized from Carpenter, we now both know the same amount of neuroanatomy. But I kid. Gross anatomy, cellular anatomy, blood supply, meninges, fiber tracts, cranial nerves, and, of course, all of your favorite encephalons (including tele, di, met, and meta). They're all here. Nosce te ipsum, as the Oracle said (albeit in Greek not Latin).

See it on Amazon