Chicago’s 3D Printer Experience: On Ratus plasticus, 3D Natives, Lions with their Heads Screwed on Straight and Topology Optimization

I would know that rat anywhere. The curve of his spine, the delicate perfection of his rib cage, legs bent in classic rodent crouch and that built-for-mischief rodent skull. The rat, or, more specifically, his white plastic skeletal facsimile, is a star, a celebrity whose photo has been splashed all over geek publications, including Wired magazine. 

So when Tom Burtonwood, master printer at Chicago’s brand spankin’ new 3D Printer Experience (3DPX)—a hybrid store, workshop and studio/classroom—handed me the plastic skeleton, almost literally hot off the press, it was like meeting an old friend. The magic, of course, is that Ratus plasticus (not its official name…), who was a mere 10 months old when he made his history-making voyage through a medical CT scanner, is very likely still alive, white fur and adorable whiskers intact. 

Almost 120 years after the accidental discovery of the X-ray gave us a way to peer inside bodies sans scalpel, it is now possible to recreate exactly what’s inside—and to make copies wherever and whenever we’d like. Ratus plasticus is immortal, an instant artifact slicing through time, space and imagination.

“We are like archaeologists,” notes Burtonwood, “but unearthing objects from the future.” Or recent past. Or, since virtually anything can be scanned, ancient history. Burtonwood, who also teaches at the School fo the Art Institute of Chicago, began to experiment with 3D printing by scanning pieces from the museum’s collection, turning them into plastic tchotchkes. Not even the iconic lions were safe…

The playfulness of the objects masks the serious potential of the technology. The lion’s screw and socket system, for example, was designed on a computer and printed so precisely to spec that the head twists on perfectly straight. 

Likewise, the popular “head scans” offered at 3DPX, are a kind of “gateway” amusement. It is fun—and funny—to stand on a platform in the window, spinning in place for a scan. But when you see a file of you in neon green being twirled and tweaked on a computer screen, your every gesture mimicked to perfection, the ramifications of what just happened begin to sink in. Mini-me is a kind of clone.

At least on the surface. The literal strength of additive manufacturing—as 3D printing is also called—is on the inside. “Topology optimization,” to use the fancy term, is about finding the perfect balance of strength and lightness, often biomimicking nature. 

“…The results of topology optimization are structures that have outward dimensions identical to normal load-bearing elements such as beams, yet have interior dimensions that look very different from traditionally manufactured parts.  In place of triangular or circular voids, these parts have remarkably organic, almost bone-like shapes. The reason is, topology optimization software systematically analyzes the stresses on these shapes and then removes the most superfluous material from the design. This process is repeated over and over by the optimization software, and by the end the computer design leaves only a skeletal interior structure…”

—Brian H. Jaffe, Topology Optimization in Additive Manufacturing: 3D Printing Conference

Additive manufacturing is a whole new way of thinking about how things can be created, whether it’s rat skeletons, fashions, or buildings. And just as there are “digital natives”—children who never knew a world without smart phones, touch screens and tablets—there will be “3D natives,” for whom the miracle of printing objects will simply be a regular part of everyday life.  

Indeed, a new middle school tech academy set to open in Charlottesville, Virginia, will have one 3D printer for every four students. Charlottesville is a pioneer, but as the costs of printers, scanners, computer software and feedstocks keep dropping— in no small measure due an onslaught of virally popular crowdfunded projects on Kickstarter and Indiegogo—more schools will follow.

Almost every day—and from seemingly every part of the globe—someone is coming up with a nifty new way to play with 3D printing. For example, Doodle3D from the Netherlands, provides a child-friendly way to turn drawings into objects, no computer programming experience required. Tellingly, though, as the company’s Kickstarter video shows, it also brings out the inner-inventor in adults as well. 

“I still think it’s a little miracle,” says Frans Beelen, who designed a colorful handle to more easily carry several shopping bags at once. 

Yes, Frans, it really is. 

– J. A. Ginsburg / @TrackerNews

RELATED: 

• 3D Printing of Preclinical X-ray Computed Tomographic Data Sets / Journal of Visualized Experiments (JOVE) / video & scientific paper
• Shapeways, MakerBot, and Lux Capital Stoke Ambitions for 3-D Printing / João-Pierre S. Ruth / xconomy

3D Update: Try This at Home / Biomimicry edition…

Great tech innovations have a way of morphing from gee whiz wonder to part of the daily landscape in the blink of a cyber eye. Life before smart phones and tablets? Barely imaginable. Life before the Internet? Really? 

The current torrent of 3D printing breakthroughs is a little different. The gee whiz came with the realization that it could be done by almost anyone. Now it is about the riff and variation of what to print (houses? body parts? guns? tchotchkes?) and how to turn almost any material into a 3D “ink.” 

What’s amazing is that it is not surprising a rat skeleton can be printed from a scanned live rat: We have come to expect the miraculous, though still marvel at the detail. 

3D printing is a multi-disciplinary playground, where the outlandishly imaginative is applauded, experimentation encouraged and a sense of fun seems to permeate everything. Led, and perhaps liberated, by a joyous makers’ ethos that made a thriving Thingiverse possible, the 3D revolution is driven not by a tech elite, but rather the universal human need to create. 

The tools and software for 3D printing are getting simpler and cheaper all the time. Comparatively inexpensive laser scanners designed for home use, such as Makerbot’s Digitizer and Indiegogo favorite, the Photon 3, are just months away from market. Paired with open source software compatible with Mac, PC and Linux, these scanners will uncork yet another round of inventive genius.  

 (T)he Photon isn’t just for 3D Printers, it’s the best tool for 3D animators, designers, hobbyists, prototypers, engineers, or anyone in the business of 3D creation. It’s perfect for reverse engineering, prototype development, duplicating objects, modifying existing products, archiving, generating content for video games, experimenting and so much more. Scan models, tweak them or combine them. The options are endless.

—Indiegogo

Biomimicry

Biomimicry is the ultimate cheat sheet: mining eons-worth of evolution for a fast insights to design problems. Nothing iterates like nature. 

Strictly speaking, the printed rat skeleton was copied rather than bio-mimicked, but it is hard not to consider the potential in light of two other recent breakthroughs: printing cell-like material complete with pores that provide nervous system functionality; and self-assembling materials inspired by the ways proteins fold, create using “4D” printing (time is the fourth “D”).

Each technology is remarkable in its own right. Imagine a surgeon printing a scan of a patient’s organs and bones before an operation, or a doctor printing “cells” for artificial tissue to treat a burn victim. And with materials that self-assemble, it’s a hop, skip and jump to thoughts of the Singularity. 

What if you could combine them, using a Photon scanner and a Makerbot printer…at home? 

What would Yoda, Star Wars sage and resident Thingiverse poster geek, say? 

“Me real make! I live want to! Hmmmmmm.”

RELATED: 

• The Yoda-speak Generator
• Yoda Thingiverse page
• Biomimicry 3.8 / Janine Benyus’ web reference
• Self-Assembly Lab / website

— J.A. Ginsburg / @TrackerNews

The End of the Beginning: The Starter League and Beyond

No one wanted to leave on Friday night. The Starter League Class of Winter 2013 clustered near the entrance of Chicago tech hub 1871 for a long time after the “Starter Night” festivities wound down. We were a herd of newly minted proto-developers in black hoodies, not quite ready to be history. After 11 weeks of having our brains bruised and battered by the quirks and complexities of computer code, we were just starting to get the hang of it, starting to get good at working together, starting to see the potential. 

Which, of course, was the point. It is a “Starter” League after all, designed to get students “from zero to one.” Personally, I only made it to 0.5, but many of my classmates became remarkably adept—indistinguishable from the more accomplished entrepreneurial geeks glued to their laptops, draped over every surface at 1871.

••••••••••••••••••••••••

For the first time in my life, I found myself on the wrong side of a learning curve, a feeling that was alternately horrific, humbling and weirdly wonderful. Trying to figure out HTML/CSS  felt like learning how to knit in the dark. Knit one HTML, purl two CSS, then jump over to a browser to see if it worked. 

I am not a terribly good knitter even with the lights on. Yet, despite my striking lack of natural gifts, I am not done with the digital yarn. The logic of the code’s illogic somehow osmosed its way into my fingertips—enough that I think I can do this. I may never be great, but then my objective was always about communicating better with front end developers, not displacing them. 

Still, it has been profoundly unsettling to realize that the codes that run our lives are such a tangle. It turns out that behind the smooth sleek curtain of tech, there are legions of nerdy wizards scrambling to come up with fix after fix after fix. The code for CSS (cascading style sheets), for example, is such a mess, we were taught to cut and paste a “reset” at the top: a long patch of code designed to clear out decades of accumulated cyber plaque. 

Likewise, we learned to include parallel commands to accommodate a variety of browsers because Firefox, Safari and Chrome all “hear” things a little differently. At the same time, there can be several ways to code the same command—some considerably more convoluted than others—which creates the equivalent of digital dialects. Things can—and do—get lost in translation. 

There is a very good reason that the questions on the Starter League’s application focus so heavily on persistence. You will tear your hair out and mutter obscenities at the screen. You will struggle to figure out how to explain the problems you’re having. And when the least little thing goes right, you will feel like the master of a (very small) universe. 

•••••••••••••••••••

The Starter League’s ethos is everything you could hope for. There is a genuine culture of support. But the optimism that everyone can become proficient at coding is a little rosy. It really is beyond most of us to get even moderately good at this.

HTML / CSS. Python. Ruby. Rails. Javascript. PHP. Codes woven together. Nested into one another. Syphoning data from API’s. Dancing a Github polka two-step waltz. 

For all the attention to website user experience (UX), precious little seems to have been aimed at improving coding UX. I found myself wondering: Where was the visionary—the Steve Jobs of developers—who would banish “clear fixes” and other such tortures to usher in an era of intuitive user-friendly coding?

It could be a long wait, so I will continue to knit badly until I knit better. The “weirdly wonderful” part of being so inept in class was the realization that everyone, including the teachers, still struggles. The ones who succeed just don’t let the potholes stop them. 

So I have started to open doors that, prior to TSL, I would have left shut. The recent Chicago Women Developers get together at Google for International Women’s Day was a revelation. What a remarkable group! I can practice HTML/CSS at “XX hack nights,” and, once I am a little more confident, perhaps take class in javascript or python. 

I also plan to check out the Tuesday evening OpenGov hack nights at 1871. I came across this group during an HTML class break and, gracious, it’s another pod of brilliance. You don’t have to be a great coder to be a part of it, either, just willing to parse through data and figure out ways to be helpful.

Finally, I will lobby Shay, Rhagu, Neal and Mike for a Starter League HTML/CSS weekend boot camp for those of us still struggling to get to “one.”

I know I can do this…

APPINESS

A major part of TSL experience involves joining a team, ideally made up students from across the range of classes—HTML/CSS, Web Dev, UX and Design—to collaborate on building a real live app. 

Imagine the first day of band practice in third grade and you’ll have a pretty good picture of how things start out. None of us really knows what we’re doing, and now we’re doing it together.

Amazingly, this works. Eighteen teams presented Friday night. Several of the apps were quite good, among them Operation Overlord, a second screen reference app inspired by the WWII HBO series, Band of Brothers; NugHub, a GrubHub clone for dispensary marijuana that might one day make a fortune; and the delightfully designed Sinkup, an app for scuba diving in Lake Michigan. 

I joined the Parent Leader Toolbox team. The group was already pretty far along with design and programming when I came on board, but needed help developing content—a comfort zone for me. 

The inspiration came from a book called How to Walk to School, detailing the efforts of a group of East Lakeview moms to improve Nettlehorst, their neighborhood elementary school. The app was designed to pick up where the book left off, providing case studies, templates, tips and resources to help parents groups at other schools. 

For Starter Night, the app was a handsome rough sketch. But it may grow to be much more than that. In April, several team members will meet with some of the moms to figure out next steps. Should this be a website? Should this be a digital book? Both? The format will need to be mapped out, a production strategy developed and funding options brainstormed.

It really is remarkable to think that a group of people who didn’t know each other three months ago could pull this off. There is still a long way to go, but we have made a start. 

Onward!

—J.A. Ginsburg / @TrackerNews

RELATED: 

• The Starter League, Moxie Jean & TechStars Chicago on WBEZ (sound cloud files)  / Built in Chicago post / J.A. Ginsburg\

• A Juncture in the Narrative: The Starter League, CSS/HTML and Me…  / TrackerNews Dot to Dot / J.A. Ginsburg

• On Order from Chaos and Purpose from Principle: Holovaty, Victor and Connections / TrackerNews Dot to Dot / J.A. Ginsburg

A Solstice Encore: Imaginary Carl Sagan, a Holiday Mix Tape and the Tannahill Weavers

A few years ago, Maria “Brainpicker” Popova and Mel Exon of BBH Labs put together an online holiday mix tape. Friends were asked to claim a date, suggest a song and write something about the season. I drew the winter solstice, December 21. What a hoot.

This year, I was so distracted by the Mayan media frenzy, I nearly forgot the date had another meaning.

I’ve reprinted my entry below, but to see it in all its original Taped Together glory, click here and page down to the 21st.

Happy Solstice One and All!

“If Carl Sagan had lived long enough to have owned an iPod, what would have been on it?”

In my quest for the perfect solstice song, I found myself channeling a dead astronomer, hoping for inspiration. I had learned—the hard way—that solstice music as a genre is dominated by the tenderizingly sweet sounds of New Age artists. Alas, I am Old Age and, apparently, diabetic.

I briefly explored the limited but promising niche of hibernation songs. I thought about my friends who had married on this day-of-longest-night many years ago. So brilliant. I tried conjuring up Chinese astrologers, Egyptian priests, Aztec mathematicians and, of course, those henge-loving Druids. Surely they must have chanted or hummed or sang or drummed as they witnessed time writ cosmic in the swinging perfection of the planet’s seasonal pendulum? Sadly, nothing that has survived to rank on Amazon…

Finally, I asked Imaginary Sagan.

“Good Morning, Starshine?” he offered, apologizing for having come of age in the Hair-y Age of Aquarius.

“H’mmm. Might work in the southern hemisphere, where it’s turning into summer, but it’s not festive enough.”

“Let’s go to the pub,” he suggested. “You wouldn’t believe how many award-winning thoughts I used to have in pubs. Billions and billions of them.” And he was right. Sitting in the cozy glow, with laughter and live music and the cold Chicago winter on the other side of the door, I watched a parade of Imaginary Ancients troop in, grateful for a pint and some company. It’s a big, cold, lonely universe out there.

So it’s the last call of the night, the last call of the last season of the year. Close your eyes. You are in a pub somewhere in Scotland. You are surrounded by friends, feeling warm, rosy, loving and loved. Now, raise your glass and sway along to The Tannahill Weavers singing “Auld Lang Syne” in deliciously indecipherable Scottish. Here is to you, Robert Burns. Here is to you old friends, stars all.

— J. A. Ginsburg

File Under “Good, Evil and the Neutrality of Tech”…

Two stories that spun me awake this morning, zipping through Zite and flipping through Facebook…

Harvard archeologists literally reconstruct the past with 3D tech (via Wired):

…”This is conservation and protection for the cultural world similar to that undertaken for the natural world,” Greene says. “3-D imaging can be used not only for objects, but also for standing monuments. Basically, broader access to 3-D scanning tools could create a kind of “version control” for material culture…”

Congressman calls for a ban on 3D printed guns. So, a problem that you didn’t know existed with a solution that won’t work. Great. (via Boing Boing)

…The congressman points out (correctly) that all-plastic 3D printed weapons would not be easy to spot using traditional methods, such as metal detectors….

The good news? Civilizations destroyed by build-a-guns can be reconstructed in a lab for future study.

— J. A. Ginsburg / @TrackerNews

RELATED

• The Fab Age: 3D Printing, Biomimicry, the Moon and More! by J. A. Ginsburg / Dot to Dot

On Imaginal Disks and Innovation: Business Lessons from the Science Pages

The poetry of metamorphosis is inescapable, even when pared down to the “just the facts ma’am” bare bones science. The transformation of chubby grubs into precision aerialists, or hungry caterpillars into nector-sipping butterflies and moths, or fish-ish tadpoles into operatic frogs is as matter-of-fact and breathtakingly wondrous as Cinderella’s pumpkin-turned-carriage and mice-turned-footman.

Surely there must be a wand involved. 

Metamorphosis, of course, is the original metaphor, and so mesmerizing and powerful that understanding the mechanics doesn’t seem to diminish the mystery. 

How does a caterpillar rearrange itself into a butterfly? What happens inside a chrysalis or cocoon?

First, the caterpillar digests itself, releasing enzymes to dissolve all of its tissues. If you were to cut open a cocoon or chrysalis at just the right time, caterpillar soup would ooze out. But the contents of the pupa are not entirely an amorphous mess. Certain highly organized groups of cells known as imaginal discs survive the digestive process. Before hatching, when a caterpillar is still developing inside its egg, it grows an imaginal disc for each of the adult body parts it will need as a mature butterfly or moth—discs for its eyes, for its wings, its legs and so on. In some species, these imaginal discs remain dormant throughout the caterpillar’s life; in other species, the discs begin to take the shape of adult body parts even before the caterpillar forms a chrysalis or cocoon. Some caterpillars walk around with tiny rudimentary wings tucked inside their bodies, though you would never know it by looking at them.

— Feris Jabr, Scientific Amerian

Imaginal disks. Imagine that. The metaphor goes even deeper. 

Now imagine this: Metamorphosis is closer to a rule rather than an exception of life on Earth: By some estimates, as many as 90% of all insects (which dominate in the species count) shape-shift. Add in a few vertebrates and the tally may be as high as 65% of all species. 

Scientists are still puzzling the “why” details, but one theory suggests that by seeking different food sources, youngsters and the adults are not competing for the same limited resources, so there is literally more food to go around. 

IMAGINAL INNOVATION 

I have been thinking a lot about imaginal disks and innovation over the last few weeks: the unseen latent potential to transform from one business to another—a service to a good, a good to a service, past as prologue. 

“Think different”—Apple’s famous tagline—turns out to be the rallying cry of all things imaginal. It would have taken a sharp eye to have seen 20 years ago the proto music / video / books service, the smart phone empire or the tablet revolution within a niche player computer company. Of course, those developments depended on improvements in web technologies and bandwidth—which, to stretch the analogy, are a kind of new food source. Those proto-businesses were there, waiting for the right moment, the right environment, to grow. 

TO BE(E) THIS, OR TO BE(E) THAT: more from the biomimic business beat

Genes, it turns out, are more of a rough template of possibility, rather than roll-of-the-die certainty, and that the dance of Nature versus Nurture is considerably more dynamic and subtle than previously thought. 

Honeybees are the ultimate “twins” study: all the workers in a hive are genetically identical. Yet some spend their lives serving the queen, while others flit among the flowers. If it is not written in the genetic code, what determines this division of labor?  

This is one of those sleeper stories snoozing in the “sci-tech” section, but one that really, truly is quite a big deal with ramifications that go on to the horizon. 

Think of genes like little light bulbs that can be toggled on or off. A gene exists within an environment and changes in that environment can determine whether it toggles on or off. This is called epigenetics, ”the study of heritable changes that occur without a change in the DNA sequence” (epi from the Greek word meaning “upon”). In  other words, outside factors can affect genetic expression.

These toggle on/toggle off states—and the traits that they program—can be inherited, which is petty amazing. Perhaps even more amazing, though, is that these states and traits can change within a single lifetime. 

…(A)nalysis of the worker bees’ DNA revealed that foragers had one pattern of chemical tags on their genes, while those that stayed home had another. When bees swapped one job for the other, their genetic tags changed accordingly. Scientists call these patterns epigenetic states, because they work on top of the normal genetic code.

The study is thought to be the first to show that reversible chemical markers on genes might drive different behaviours in a living creature.

—Ian Sample, The Guardian

From the itty bittiest of cellular micro, to the macro of planetary climate change, environment can determine destiny. 

Is your head spinning yet? 

BACK TO BUSINESS

For the last year, I have been following the tech startup scene in my hometown Chicago fairly closely. There are about a dozen businesses that I have found particularly compelling, not just for the needs they address (although SpotHero, every time I pay less for parking downtown, I am so darn happy…), but also for their “imaginal disks.” The businesses that will go the distance will be those able both to scale up, and also have the potential to scale out: to transform and grow into suites of new businesses. 

Whether it is a travel service with a Harry Potter-ish potential that can grow its business as its target clientele ages (Travel 720), or an academic publishing platform that opens the door for all kinds of new journals (Scholastica), or a children’s clothing business that is building valuable “network equity” as it expands (Moxie Jean), these businesses are rich with latent possibilities. 

Like the bees, they have all the genes. We’ll just have to wait and see what toggles on. 

— J. A. Ginsburg @TrackerNews

RELATED: 

• How Did Insect Metamorphosis Evolve? / Ferris Jabr / Scientific American

• Biomimcry Institute (website)

• Ghosts in Our Genes / Epigenetics excerpt / NOVA (video)

• Think Bigger / J.A. Ginsburg / TrackerNews Dot to Dot

• A Chicago Tale of Parking, Innovation, Bad Deals and Better Options / J. A. Ginsburg / TrackerNews Dot to Dot

• Publish, Perish & Disruptive Innovation: Scholastica’s Better Answer / J. A. Ginsburg / TrackerNews Dot to Dot

• Baby Clothes, Sharing, Paradigm Shifts & Collaborative Consumption (with addendum, 2/17/12 / updated 9/12) / J. A. Ginsburg / TrackerNews Dot to Dot

Life at 10x and Beyond: Lichens, a Liverwort, a Microscope and Me…

(from the archives: This article was originally posted in July, 2008 on an iWeb blog called Germtales. Germtales went into cyber-hybernation. iWeb gave up the ghost… - j.a.g.)

It was bound to happen. The only wonder was it hadn’t happened sooner. Someone finally sat me down in front of a microscope and said, “Look!”

It was a “British Soldier” (Cladonia cristatella), a wee little thing, like the lichen in the photo above, with a bright red “fruiting body” cap. Aided by the unabashedly nosy lens of a dissecting microscope, I could see into all its folds. I could study the texture of its improbably lurid top, which “real size” was smaller than the head of a pin. Armed with a thin probe—the club from hell under magnification, especially with my clumsy touch—I could peer into all its secrets. The next few hours were lost in Lilliputian delight.

While lichenologist Rich Hyerczyk… No, that doesn’t do him justice. While Rich Hyerczyk, a lichen connoisseur and teacher of the “Lichens All Around Us!” class at the Chicago Botanic Garden, patiently took us through the basics of key guide identification, I happily oohed and ahhed, content for the time being simply to see these things exist.

Foliose. Crustose. Fruticose. The general shape-based classifications were fairly straightforward (looks leafy, looks crusty, looks shrubby). After that, it was alien territory: new words for previously unimagined things.

Soredia. Thallus. Xanthomendoza. Physcia. Candellaria. Squamule. Apothecia. Podetia. I was a stranger in a strange land and pretty darn happy about it.

One of my favorite parts of travel is taking a walk alone as soon as I arrive somewhere new—before anyone has a chance to tell me where I am.

Within minutes of stashing bags at a hotel in Bologna, I am exploring the side streets off the main square, finding book stores (five in 30 minutes, including the magnificent Biblioteca Salaboursa—where I could have lived happily ever after), gelato shops, bakeries, one notably saucy fountain, a few tucked-away churches and some fabulous street theater.

In Havana (scouting a segment on the Old Havana neighborhood for a sadly never-produced National Geographic series on the “World’s Most Endangered Places”), I walk along El Malecon to see the sea. A honk from at least a block away jolts me from my shimmery thoughts: The driver of a 1950-something Buick with question-mark brakes warns me to safety.

LICHEN-LAND

Traveling to the land of lichens has been every micron as interesting and unexpected. Like many good journeys, this one began with a wrong turn and a touch of serendipity.

This past spring, groves of miniature and somewhat Seussian palm trees took over an old strawberry pot I use for moss roses. I put off planting for weeks, so adorable where their charms. Thinking they were lichens and wanting to know more, I signed up for the class.

Alas, my erstwhile lichen turned out to be liverwort—Marchantia polymorpha—but no matter. I was hooked on these strange little lichen plants and completely enthralled by their symbiotic society of fungi, algae and, every once in a while, cyanobacteria (microbes with a talent for photosynthesis).

A lichen doesn’t have parents so much as partners. An estimated 13,500 species of fungi seek out just a handful of algal species (and cyanobacteria) to capture and nurture in order to harvest the sugars they produce. In turn, the algae, now protected by fungal armor, are given the opportunity to travel, colonize and conquer the world. These odd-couples can make a go of it just about anywhere. There are lichens on rocks in the Arctic that live for hundreds and even thousands of years. In fact, crustose lichens—the ones that grow on rocks—are literally one with their rocks. The line between inorganic and organic is breathtakingly modest.

If you split a lichen’s fungus and algae apart, the fungus will die while the algae survives —provided there is enough water and conditions are right. It is basically the same story, writ larger, with humans and our commensal, “beneficial” microbes. Lose the gut bugs that help with digestion, produce Vitamin K, and, by their very presence, keep “bad” microbes at bay, and we’re toast. Microbes on skin, teeth, in vaginas and other surprising places play equally key roles. (Women on antibiotics are more vulnerable to yeast infections because the microbes that keep the yeast in check are gone.)

Birds, bees, alligators, cows, snakes and puppies — the animals need the microbes, but the microbes don’t necessarily need the animals.

It gets a little easier to accept the role as the “fungal half” when you start to see Life more as a series of social networks than tooth and claw competitions. Lynn Margolis (whose biology/geology-spanning career is itself as symbiotic as what she studies) and her son, Dorion Sagan, have written several books detailing the Nature’s propensity for partnerships. Symbiosis rules, right down to the cellular level and even into the genome (Symbiotic Planet, Acquiring Genomes).

IN THE FIELD (OR NEARBY…)

Most of the lichens around Chicago are on bark or wood, so we took a short field trip to a patch of forest on the Garden’s grounds. It took a while for the class to get beyond the parking lot. We spent half our time scanning the bark of a particularly lichen-friendly locust with our 10x loupes and magnifying glasses. Everywhere we looked—even on concrete curbs—we found thriving colonies of lichens.

It was a rainy morning, which puffed up the lichens’ algae, making colors more intense. We went through the key: Was a lichen foliose or crustose? (only one fruiticose that day). Was it easy to peel off the substrate surface? Was it greenish or yellow? What color was its underside? Did it have apothecia (cups full of spore-filled sacs) or soredia (fringes of fungal/algal cells ready to blow away and reproduce)? We identified 29 species in 3 hours. We learned that Anisomeridium polypori gives White oak its white bark. We even found a lichen, Phaeocalicium polyporaeum growing wiry black fringe on a “turkey tail” fungus (Trichaptum biforme). In the realm of the alien, this one stood out: Its fruiting body readily apparent, but the exact location of its body body still something of a mystery.

After class, I spent another hour and a half wandering the Garden alone, loupe in hand, kneeling over benches and cement walls, assuring my future as an eccentric. I marveled at “LBM’s” (little brown mushrooms) dotting a lichen-covered linden tree, noted the relative giant-ness of mosses, and followed the intrepid trekking of ants and spiders. The Garden was filled with dozens of species never mentioned on identification plaques. Everywhere I looked there was more. I was Horton. And boy was I hearing a whole bunch of Who’s.

•••••••••••••

The analogy turned out to be uncomfortably apt. Despite their ability to survive on the most forlorn surfaces in the harshest of climates, and despite their seeming irrepressibility, it turns out some lichens are, in fact, repressible. In the presence of sulphur dioxide and other man-made pollutants, some species pack it in and disappear, making lichens good, easy-to-monitor indicators of environmental health.

But it goes even deeper than that. Dozens of bird species, along with some small mammal species, seek out lichens to line nests and burrows, possibly as a defense against disease and parasites. There are hundreds of active compounds in lichens, some of which are antibiotic. Usnea, for example, is a staple of Chinese and homeopathic remedies. Then there are the reindeer that live on a diet of lichens. Kill the lichens and Santa will have to find alternate transportation.

PATIENCE AND POSSIBILITIES

Back in the lab on the last day of class, we were ready for the 100x microscopes - the ones designed to reveal the daintiest of details. I was given a note card onto which a few chips from a picnic table had been glued back in 1992. I carefully squirted a drop of water onto some unpromising round black bumps I was told were the fruiting bodies of Amadina (nee Buella puntata) and watched as they gelled up enough to tease off with a probe and place onto a microscope slide. Another drop of water, a slide cover and a firm press to break open the fruiting bodies and we were ready for a look-see. Amazingly, stunningly, gobsmacking miraculously there they were: 8 translucent spore sacs to a bunch, just as advertised.

My bench-mate managed to find an actual individual spore. It was perfect. Who knows whether it was viable, but it might have been. Sturdy cell walls. Distinct cell markings where they were supposed to be. Life goes on.

As I drove home that night with the windows rolled down, listening to cicadas and glancing at summer-sky stars, it seemed a given that life would be everywhere throughout the universe. Life on Mars? Lichens on Mars? I wouldn’t bet against them.

—J. A. Ginsburg / @TrackerNews

RELATED

• Lichens of North America (link-filled website / photographs)
• Lichen / Wikipedia article

Photo credit for Suessian Liverwort and the Lichen on Tree: J.A. Ginsburg / CC BY-NC-ND

Publish, Perish & Disruptive Innovation: Scholastica’s Better Answer

Disruptive innovation is fun—especially when the industry being disrupted is hopelessly lame. Few industries can match academic publishing on that score: (in)famously slow, pricey and capricious. Scholars, or their university departments, can pay thousands of dollars to submit a paper for review, then wait months, or longer, to find out whether it has been accepted, and then months, or longer, navigating the back and forth of peer review. When a paper finally is published, more often than not, it is sequestered behind a high subscription pay wall, inaccessible to those who might benefit most from the research. 

“Publish or perish”—the time-honored credo of academic upward mobility—has been turned out on its head. One could perish, or at least go broke, trying to publish. 

Thousands of scientists, including a trio of Fields medal-winning mathematicians, have staged a boycott of Reed Elsevier, one of the largest academic publishers, citing intolerable greed and monopolistic practices. When the world’s top math geeks can’t make sense of the numbers, you know something’s really wrong 

Free open access journals such as the Public Library of Science (PLoS) provide a publishing alternative, but the real game-changer may come from Chicago-based startup Scholastica, which provides a low cost, easy to use, fast and feature-rich publishing platform.

Setting up a journal is free. Scholastica’s revenues come primarily from submissions fees, which cost just $5 for a law review and $10 for an academic paper. Although the law review price is actually higher than average, the research paper fee is orders of magnitude cheaper. 

Peer review, the cornerstone of academic publishing, relies on reputational currency. Reviewers are unpaid scholars who take on the onerous task analyzing others’ research both out of professional interest and to increase professional stature.

Scholastic offers an advantage here as well. The web is brilliant for tracking reputational currency. From AirBnB and TripAdvisor to TaskRabbit and Facebook “likes,” we have become a culture that loves to share ratings. 

The nuts and bolts of putting together a first rate journal still require considerable effort, but with costly and time-consuming logistical hurdles removed from the equation, the focus can go back to the mission: documenting and sharing knowledge. 

Although journal publishers using the platform can charge subscriptions if they choose, the lower cost structure means they still out-compete traditional publishers on price. They can also have an ongoing publishing program, pushing out new articles all the time, rather than waiting for a set pub date. 

Together with online educational services such as Coursera, video tutorial pioneer Khan Academy, the Open Science movement, and the emergence of an open source textbook market, Scholastica is part of a tech-enabled trend that challenges the educational status quo. This goes beyond offering an alternative to expensive educations that fewer and fewer can afford. It is about better ways to teach, learn and share research. 

Still, the forces of academic inertia are among the strongest in the universe…

…The biggest obstacle is the role that these journals play in academia itself, and how important publishing in a specific journal can be when it comes to promotions, granting of tenure, research grants and other aspects of academic life. Even some researchers who support the Elsevier boycott have said they will continue to publish in its journals because they feel that they have to.

Until that structure changes, or until enough researchers and academics decide they don’t care about the system and start to publish their work freely, the current system is unlikely to disappear any time soon. But just like the rest of traditional media industry, it is looking shakier and less stable all the time.

— Mathew Ingram / GIGAOM

•••••••••

As a platform, Scholastica is neutral: One could create a journal about almost anything. The Journal of Makerspaces, for example. Or The Journal of Urban Farmers, or Tech Incubators, or Pets, or perhaps The Journal of Humanitarian Tech. Transparent reputational currency can be used determine value, making it easier for readers to sniff out bogus, politically slanted or corporate-sponsored research. 

Just stay clear of the shady practices of Nicholas Ivanovich Lobachevsky (which, it should be pointed out, would get one booted off the Scholastica site as a TOS violation) and you’ll be fine: 

RELATED:

• Team Scholastica bios (University of Chicago grads on a mission…) / website

• A talk with Rob Walsh: Will Scholastica disrupt academic publishing? / COGSCI

— J. A. Ginsburg / @TrackerNews

Bouncing Onward: Climate, Consequences, Crops, Memes & Resilience

It is amazing what summer soaker can do. Three or four of such storms over the course of a few days can bring back the seemingly dead. For weeks I have given feeble garden hose life support to frying hosta lilies and parched grass, always making sure to water a spot near a robins’ nest so the parents would have a fighting chance of finding a few worms and grubs to feed their peeping young. Some days, the water in the hose would get so hot, I would spritz the sidewalks for few minutes to avoid scalding the already scorched.

Now it’s all green lawns, revived trees and perked up posies, reveling in gloriously normal temperatures that gently rise into mid-80s during the day and settle into the 60s for snugly cicada-serenaded sleep at night.

This is summer as it ought to be. Summer as it used to be, at least in my little sliver by Chicago. Yet even though the view out the window looks like the poster child of resilience, it is more a reminder that what was once reliably normal is fast becoming a rarity to be treasured.

Over 4,700 weather records have been broken in the US so far this year. The withered corn crop, once on track to be the largest in history will now be the largest loss in history. And with demand for all commodity crops increasing right along with global population, even little wiggles can amplify across world markets. The catastrophic floods in Pakistan a couple of years ago sent cotton prices soaring, even though Pakistan ranks a distant fourth as a supplier.

The Great American Corn Pop of 2012 is a much, much bigger deal and will translate into higher food prices, higher fuel prices (another ethanol promise broken), more hunger, more debt, more unrest and more misery in a cycle that will be tough to break.

The drought tipped the balance of a global food system already in a delicate state,   made vulnerable to petro chemical-dependent soils, fast-depleting aquifers, pesticide-impervious “superweeds,” an increasingly monopolistic agri-food supply chain, a resurgence of crop pests and rising fuel costs.

Extreme and unpredictable weather causes highways to buckle, concrete to crack, rail ties to kink, bridges to bend and rivers to become unnavigable. Even if you manage to grow a crop, there is still the challenge of getting it to market

A DANGEROUS MEME

How do you adapt to such a fast-moving target? Even if we were able turn off our collective car ignitions and switch instantly to renewable power sources, there are more than enough greenhouse gases swirling around the Earth’s atmosphere to cause mischief for decades to come. The disaster is so overwhelmingly obvious that now Koch-sponsored scientists have seen the grim light. Still, there are politicians who continue to bray for more mining and drilling.

In a tour de force numbers analysis in Rolling Stone magazine, Bill McKibben follows the money:

…We have five times as much oil and coal and gas on the books as climate scientists think is safe to burn. We’d have to keep 80 percent of those reserves locked away underground to avoid that fate. Before we knew those numbers, our fate had been likely. Now, barring some massive intervention, it seems certain.

Yes, this coal and gas and oil is still technically in the soil. But it’s already economically above ground – it’s figured into share prices, companies are borrowing money against it, nations are basing their budgets on the presumed returns from their patrimony. It explains why the big fossil-fuel companies have fought so hard to prevent the regulation of carbon dioxide – those reserves are their primary asset, the holding that gives their companies their value. It’s why they’ve worked so hard these past years to figure out how to unlock the oil in Canada’s tar sands, or how to drill miles beneath the sea, or how to frack the Appalachians.

—Global Warming’s Terrifying New Math

Sustainability, which implies a baseline stability—the very thing we are fast losing—is giving way to the meme of resilience: the idea that somehow we will be able to recover from the inevitable disaster looming and “bounce back.” It is the seductive promise of Dorothy waking up safe in her bed in Kansas, with Toto ready to resume his rightful place in her arms once more.

But the tornado that rocked Dorothy’s world is nothing compared to the tornadoes, direchoes, record monsoons, massive droughts and rapid ice melts rocking ours. Even the parched park lawn now showing signs of green grizzle isn’t bouncing back, but  evolving, bouncing onward. Weeds with better root systems are making the most of their competitive advantage. Unless someone rips up the sod and reseeds, that lawn has changed for good.

Resilience is also a neutral concept, a point that is often overlooked. What bounces onwards may not be to everyone’s liking, such as weeds, bunny rabbits, pathogens, drug cartels and oil companies.

So the question is not whether we can return to a comfortable status quo: We can’t. Rather it is Status quo vadis? Where are we going?

— J. A. Ginsburg / @TrackerNews

RELATED:

• Global Risks 2012 / World Economic Forum (pdf and additional web resources)

The Good, the Bad and the Myopic: What Nora Ephron has to do with Techweek

Techweek 2012 is a wrap. Despite some organizational stumbles, the sheer mass of programming and the crowds guaranteed good things would come of it. They certainly did for me.

Techweek ran the gamut, from Howard Tullman’s tour-de-force talk on the data-sliced present/future, full of utopian potential and dystopian risk, to Dennis Manarchy’s stunning oversize Vanishing Cultures portraits, an homage to the present/past of both people and technology. It was wonderful to meet and reconnect with people, to talk about projects, business models, progress. And god bless those ever-resourceful Task Rabbits who brought the Wow Bao buns: brilliant marketing—really, truly I will use you when the need next arises.

Yet throughout the event, there were little off-notes of sexism, most likely unintentional, but nonetheless there.

• Only 7 women on the Techweek 100 list
• An all male panel of judges for the 2012 Final Five Launch competition
• Only one woman entrepreneur in the Final Five pitch

Which is neither to say that there are not a lot of talented men on the Chicago tech scene, or that all of the men on the list didn’t deserve to be there. Rather, it is point out that the number of talented women on the scene is on the rise. And though plaid and t-shirted men still outnumbered women strolling the trade show aisles and attending lectures, I would guesstimate that at least a quarter of attendees were women. 

There are more women enrolling in Code Academy. Three of what I think are among the most promising startups in Chicago happen to be women-run:

• Sharon Schneider, Good Karma Clothing for Children
• Julie Bashkin, KLUTCHclub
• Jennifer Thomas, Travel720

This is something to celebrate. Yet when numbers skew so badly—only 7% of the techs-to-know in Chicago are women? really?—it raises questions.

I probably would have let this slide, but for a quote of Nora Ephron’s that I read this morning in an obituary. In a graduation address to her alma mater, Wellesley College, she talks, with her trademark razor sharp wit, about changes in attitudes toward women and by women since was a student in the early 1960s. Then she gets to the rather serious nut:

“What I’m saying is, don’t delude yourself that the powerful cultural values that wrecked the lives of so many of my classmates have vanished from the earth. Don’t let the New York Times article about the brilliant success of Wellesley graduates in the business world fool you — there’s still a glass ceiling. Don’t let the number of women in the work force trick you — there are still lots of magazines devoted almost exclusively to making perfect casseroles and turning various things into tents.

Don’t underestimate how much antagonism there is toward women and how many people wish we could turn the clock back. One of the things people always say to you if you get upset is, don’t take it personally, but listen hard to what’s going on and, please, I beg you, take it personally. Understand: every attack on Hillary Clinton for not knowing her place is an attack on you. Underneath almost all those attacks are the words: get back, get back to where you once belonged. When Elizabeth Dole pretends that she isn’t serious about her career, that is an attack on you. The acquittal of O.J. Simpson is an attack on you. Any move to limit abortion rights is an attack on you — whether or not you believe in abortion. The fact that Clarence Thomas is sitting on the Supreme Court today is an attack on you.”

So it makes a difference. There are good things happening on Chicago’s women-in-tech front. More good things need to happen. And we all need to do a better job both seeing and acknowledging them.

—J.A. Ginsburg / @TrackerNews

(originally posted on Built in Chicago)