Chromatophores - of chameleons & cuttlefish cousins

Chromatophores are highly specialized cells that allow an organism to change the hues and patterns of its skin.  Examples of this trait in species distantly related across the genetic tree of life, living in very different environments, argues in support of natural selection and the theory of evolution.

The chromatophores in the skin of many cephalopods exhibit polychromatism. As an example of the common mechanism, Loligo pealeii color cells are manipulated by a wagon-wheel of muscles (between 15 and 25) that encircle and stretch the central, elastic pigment sac, pulling it from a tiny sphere into a disc; typical relaxed sphere diameters of 10-100 µm contrast with 0.1-1 mm when flattened into discs. When these muscles relax, the sac recovers its original shape1. Various colors of pigment sac exist, each with a specific layer and size of chromatophore: yellow rates smallest, brown the largest. The sac transition from “off” to “on” requires approximately 700 milliseconds, and Japanese researchers propose that Sepioteuthis lessonianas' enjoys direct control over its body color and pattern, as neural signal frequencies correspond to shifts.2

The chromatophores in the skin of many lizards of family Chamaeleonidae accomplish color and pattern change in a very different way. Pigments in these cells are stored in fatty sacs called vesicles, and are not manipulated by muscles but by hormonal domino effects.  Chameleon chromatophores release their stockpiled vesicles when triggered by these chemicals, which drift about and soon burst, scattering “dye” molecules throughout the cell to temporarily alter its color. Below a transparent outer skin layer, these pigment cells are stacked vertically with respect to their vesicle “paint palette”. Yellow xanthophores are topmost, followed by red erythrophores, blue iridiphores (which use guanine as their “paint”), then finally melanophores, employing melanin to create browns and blacks. Amazingly, this dying process is additive, with greens and oranges possible from xanthophores reacting in sync with iridiphores and erythrophores.3

Both of these far-removed families of organisms utilize endogenous dyes, but this is where their isomorphism ends.  Chameleons alter integument by expending and mixing vibrant chemicals, while octopi, cuttlefish and squid are more economical, having devised stretchy, reusable pigment sacs to unfurl with motor impulses. The “bombs of paint” technique versus the “hoist the flag” approach is a fascinating example of widely divergent evolutionary lines selecting similar color-altering talents, yet employing very different cell designs in the two. The hypothetical direct neural control seen in cephalopods further contrasts with the endocrine and limbic drivers in Chamaeleonidae chromatophores; such structural control differences suggest intentional color shifts in the former, versus emotional and reactive in the latter. Yet regardless of the regulation of these two systems, their similar function supports the claim that natural selection yields maximally efficient, and often convergent, structures.

1. Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores.

Keith M. Kirkwood, Eric D. Wetzel, George Bell, Alan M. Kuzirian, and Roger T. Hanlon

Proceedings of the Army Science Conference, Orlando, FL, 29 November 2010.

2. Suzuki, M., Kimura, T., Ogawa, H., Hotta, K., & Oka, K. (2011). Chromatophore Activity during Natural Pattern Expression by the Squid Sepioteuthis lessoniana: Contributions of Miniature Oscillation. Plos ONE, 6(4), 1-8. doi:10.1371/journal.pone.0018244

3. High Dynamic Range Image rendering of color in chameleons' camouflage using optical thin films. Mark Prusten.  Proc. SPIE 7057, The Nature of Light: Light in Nature II, 705709 (August 11, 2008); doi:10.1117/12.802177

Defending Dualism (or not)

Defending dualism requires me to do what what dualist thinkers do, and postulate the existence of a type of matter-energy (proven by extensive physical research to be interchangeable at a primal level, research widely ignored by all but SF authors and New Age gurus) that has not been revealed in any scientific studies to date, ever.  While normally disinclined to shelter exclusively behind the bulwark of empirical thinking, in this case it seems the best and most honest tactic.

What is the numinous mind made of, if not of matter-energy?  And if not matter-energy, then how does it interact with the body that houses it, how does it control organs, eyes, hands or anything whatsoever?  When we spear the monstrous, easily visible neurons of a giant squid, thrusting the talons of scientific inquest into the very fibers of the biological mind, we find little that is different from our own bodies; aside from variations in scale and chemistry, the giant squids are wired very much like the elephants, the ostriches, the polar bears, narwhals, poodles, orangutans, chimpanzees, and humans of this planet.

Why, then, a separate type of elemental matter-energy for the mind?  Plato is one major champion of this dualist position, as he taught that material existence is merely the echo of a far higher state.  Our bodies, according to Platonists, are crude after-images of mystical Forms, things which also inspire music, nature, and all the ‘universal concepts’ of our manifold physical reality.  This type of thinking is possible in a world without modern science, in the Near East of two millennia ago: it seems indefensible in this age of broad physical understanding, when we measure electrochemical impulses across invisibly small gaps in living brains, forge new elements by clever subatomic manipulations.  All is matter-energy, the physicists teach us, and the dynamic, shimmering, self-gazing lattice of loops which we name “mind” is no exception.

Spinoza is fearless in his rejection of Platonic dualism, writing with astounding clarity from pre-Enlightenment Europe in his On the Improvement of the Understanding (1662),

“The properties of things are not understood so long as their essences are unknown.”  He also opined, in correspondence, “we must take care not to admit as true anything which is only probable. For when one falsity has been let in, infinite others follow” (Letter 54).  It is this sort of rigorous intellectual honesty and parsimony of argument that provide the foundations for all the brave investigations that have built our miraculous -yet rational- world of technological wonders.  It is the spirit of material monism, or materialism.  As I am pursuing a Bachelor of Science, and am planning a career in research and design, I cannot seriously endorse any position other than materialism without feeling like a fraud, and without the bile of ingratitude souring my breath.

Everyone's a loser, baby, that's true

So here I am, scribbling up a summary of this ridiculous book on our visual system.  It's a very visceral and vivid piece of writing, and it lends itself well to a sentence-to-page sort of ratio. Yet I'm only a tiny way into it, when I realize- it's all true.

Here's the gist:

Our vision “looks” for four things: the shape, the shiny, the light, and the sight-line. That’s it. These four calculations are what constitute our visual system, sole tenant of our occipital lobe. The early visual system sorts out which changes in these things are due to what reasons, and then creates images in which these reasons are easily distinguished. Got it?


These Four Factors (FFs) are so incredibly significant that our entire visual representation is built around creating them. What you see is a result of How: Shaped, Shiny, Lit, and Seen a surface is. Ah, a surface! you cry. I can grasp what’s going on here. Indeed. The physical aspects of a four-dimensional object are well represented by a model which features the FFs, for Four Factors. So our mammal primate body built us a visual system which understands the FFs.

Stage 1: the Primal Sketch. Vital information such as intensity changes, local geometry, and luminosity are encoded ever so briefly in a rough scrawl. Then, soon after, a bunch of other cool things happen to that Primal Sketch and a 2 ½-D (two-and-a-half dimensional) image is rendered- again, by the weird neurons of the occipital lobe, aka the early vision system, or V1. Then the two sketches are placed atop one another, logically, in a viewer-centric perspective.


Isn't that frustrating? Color doesn't appear until V4, by which point I've almost lost interest.  Yet I'm also reminded of how unabashedly atheistic most of this psychophysics is, and then I keep going.

volume units conversion hack

Here you go.  I feel like sharing notes from General Chemistry, if only to share my bemusement... this is a 200 level science course?  Le sigh.

Naturally, you'd write the answer differently, in proper scientific notation. ( 5.15 x 10^-3 ) I hope that scientists actually adhere to this, IRL!

Then again, until my first taste of college, I thought that all frats and sororities actually taught their members ancient Greek.  Gullibility ftw.

Last days of Summer 2012 at the Japanese Gardens

Light autumn tones at the Portland Japanese Gardens.

Lastly, the International Rose Test Garden is starting to close up for the fall.

recipe for my iPwn

So you've jailbroken your iPhone, and now have access to the Cydia store.  Isn't it cool?  I like the icon's color- brown was an interesting choice, and it really looks slick parked right next to the AppStore, which is exactly where you should place it... if you're as finicky about organizing your apps by function as I am.

Well, what happens now?  Cydia, much like the AppStore, is chock full of wonderful apps (and hacks) yet it will take some research to figure out which ones to grab.  You NEED some of these in order to take advantage of your newly-freed iPhone.  The more of these you install, the more options and functions you'll impart to your favorite device, above and beyond what the AppStore is able to provide.

Here are my recommended Cydia acquisitions.  Note that almost all are completely FREE, making this whole jailbreak-and-master process all the sweeter.  Also please note that you cannot delete Cydia apps by simply holding down on them and then choosing the Delete X that appears.  It doesn't appear over these apps, so spend a little time getting familiar with the Cydia interface: this is how you uninstall them, in the Manage tab.

Activator - The essential Cydia package to install, in my humble opinion.  While a bit tricky for those not familiar with simple programming, Activator is so powerful that it's worth the few minutes of fumbling and playing around just to get the hang of it.  Despite months of daily use I still haven't mastered it, and I doubt I'll ever discover all the useful combinations.

In brief, the idea behind Activator is to choose a situation for a certain gesture, then assign that gesture a certain command.  This is easier done than said, so futz around a bit and see what you can come up with.  Did you ever wish that it were easier to unlock your phone?  Easier to lock it?  Think practically and a few wild notions will still creep in, so get futzing!  My favorites are listed below, if you're stuck for inspiration.

• Anywhere - Shake and Bake - Lock Device
• At Lock Screen - Double Press - Unlock Device
• Anywhere - Triple Press - Flashlight (from the AppStore)
• Anywhere - Short Hold - Camera

Isn't this sick?  You can invent entirely new ways to use your phone by junctioning apps to gestures.  Have fun with this, it's somewhat like turning your phone into a futuristic army knife.


SBSettings - What does the SB stand for?  I've always assumed Speed Bar.  This is one of the definitive kits that every iPwn needs.  SBSettings is a toolbar that is revealed by swiping down from the top of the screen.  It provides direct, instant control of multiple core hardware services, like Bluetooth and Wi-Fi, and offers tons of expansibility (read: explore Cydia for more functions).  It can be configured extensively, yet it's separate from Activator so don't get confused out of the gate here.  You can even change the way it looks, if you want it to match your customized iPwn's appearance (see below).  This is a package that many tech writers name as their number one reason to jailbreak their iPhones.

Rotation Inhibitor for SBSettings - Extra function button for SBS (can't imagine why it's not default), nice to junction to some gesture, in Activator.




WinterBoard - The key to skinning your iPwn.  Need I go on?  Well, perhaps, especially if you're uncertain what skinning means in this context.  It's nothing more or less than altering the appearance of iOS, leaving the function unchanged.  Many, many custom modification designs exist on Cydia, and these mods can provide you with new sound effects and more, too.  WinterBoard's not just visual tweaks.
You'll need to fish around Cydia for icon themes, custom sound effects, and anything else fancy to beautify your favorite device.  (That FacebookBlack thing I've installed does little else but change the fb icon and make its opening screen black instead of blue!  There are some nifty and screwball mods just waiting to be discovered.)  Then just "Respring" your phone with WinterBoard and see if you like the changes.

You can also remove aspects of iOS, so play around and see if you want that Dock to be transparent from now on.  PS: Try life without icon labels on your phone for a day or two, and tell me it's not the slickest thing you've ever seen.


LastApp - A cleverly direct concept, junctions well with Activator to give you single-gesture access to the last app you had active.  Very, very good for iPads, too.

DisplayOut - is incredible.  Totally worth the $2, as it lets you output everything, every app, whatever is on your screen, to the second screen attached to your phone.  If you already watch Netflix (with your "iVCR") then you surely see the attraction here.

Genesis - I'd be selfish if I didn't share my favorite WinterBoard icon set.  Check this out, it's authored by JackieTran.  The before and after shots below should help.  (RePS: See, no icon labels!)

DreamBoard - This one's silly, and I use it as a party trick only, but perhaps a new Theme for your iPwn is in the cards?  Seriously, not a skin, not like WinterBoard- this is something different.  Again, look for Themes on Cydia (GalaxyOS is nice) and enjoy the trip!

with about 100 days left in my journal, a blog appears

Months of waffling and denying my desires to create a blog have finally ended, and spectacularly strangely at that.  Within an hour of meeting a fine new friend in a randomly selected cafe, she implored me to start a blog, to share my stories with anyone who finds them.  If I don't so it, she swore, no one else will.

She's right, of course.  It helped her argument that I rewatched Blade Runner two nights ago; Batty's death monologue flew to my mind, that line about all his experiences lost to the ages, like so many tears in the rain.  Rutget Hauer allegedly wrote his own dialogue for that scene, perhaps the most infamous of the film.

And so here I am, taking the advice of a freelance web designer AND a fictional android- I can't argue with expertise such as that.  About to resume undergraduate studies, about to move to a new apartment downtown, and now possessed of a new creative outlet.  Thank you, universe, for unexpected prompts.