Vit D: The sunshine vitamin

Vitamin D Pills by essgee51, (2010) CC By-NC 2.0 on Flickr

There are few things more miserable, albeit non-deadly, than a cold. I was sitting on my couch, nostrils taped open with a “Breathe right” strip, my achy body wrapped in an afghan. By then, I was feeling quite sorry for myself, blowing my nose, and tossing a heap of crumpled tissues into the waste basket.

As I cradled a steaming cup of tea in my hands, my phone rang. I glanced at the caller id.It was my Dad. I picked it up.

“Hello?” I hoarsely croaked into the receiver.

“Are you sick again?” My dad asked. “Haven’t you been taking Vitamin D?”

“I’ve been taking 2000 IU a day!” I protested.

“Hmmm,” he said. “Maybe you should take more.”

Vitamin D is probably one of the most underratedly awesome contributors to human health and well-being. It helps build bones, and regulate the immune system. (Aranow, 2011.) Vitamin D may also help prevent heart disease and play a role in preventing certain cancers. (Harvard School of Public Health). As a human living in a northern latitude (approx 42 deg N) during the wintertime, I am the first to admit that I am not up to synthesizing all my own Vitamin D from sunlight and/or food consumption.

Humans synthesize Vitamin D from sunlight when UVB rays hitting skin convert precursor 7-dehydrocholesterol into Vitamin D3. Vitamin D3 travels to the liver and kidneys, to be come an active form of Vitamin D (Source: Harvard Medical School, 2009)

One of the ways in which Vitamin D may boost the immune system is by activating t cells, the guardians of the immune system that spring into action when they detect “non-self” invaders (i.e. pathogens) in the body. Per 2010 research paper at the University of Copehagen, after t cells detect traces of foreign material, they must become “activated” in order to become sensitized and effective fight that specific germ. T cells send out a chemical signal that triggers production of the VDR protein. VDR brings Vitamin D into the t cell, “activating it to hunt down and bind to pathogens. TL;DR: Not enough Vitamin D? T cells will not be marshalled as quickly to fight nasty germs.

So what’s a winter-bound, higher-latitude-located human to do? I could ingest more food sources of Vitamin D, like the injured Viking chugging fish oil in the extremely entertaining historic skiing movie, The Last King. Getting naked outdoors in subfreezing temperatures for maximal epidermal sun exposure is a no-go. (Frostbite, possible arrest due to violation of public decency statues.) Also, my relatively high latitude geographic location (Michigan!) in winter would reduce the incident angle (and Vit D synthesizing effectiveness) of sun exposure.

(It probably doesn’t help that my melanin-deficient skin’s causes me to cover up even in summer. This is what I usually look like when I plan to spend any time outside even in warmer months. )

It looks like the Vitamin D tablets are my new best friends. P.S. Cold symptoms subsided after a weekend with tea, soup and self-pity. Also, probably Vitamin D.

Visit to the Conservatory

When I imagined what Michigan looked like in the winter, it was something like this:

Icy Marsh at Crosswinds by Protopian Pickle Jar (2016) CC-BY-SA 2.0, on Flickr

Turns out, as long as you put on long underwear, snow pants, sweaters, parka, hat, mittens and boots, it’s pretty fun to romp around outdoors in the snow on a sunny day. Even when temperatures are well below freezing.

But sometimes, the interminable stretches of cloudy days, intense (and not-so-intense) cold, snow and ice just start to *get* to me. Even though I put snow tires on my car, put a happy light in my living room and increased my dietary intake of Vitamin D, I begin to wonder if winter is my punishment.

To deal with the bleakness, I have been longingly poring over photos of gardens in high summer or ogling observations of tropical flora and fauna posted on iNaturalist.

After a rough few weeks, I think I have found another method of coping with Michigan winter: The Conservatory at the Matthei Botanical Gardens.

Pink flower pop by PPJ (2017) CC BY-SA 2.0

I had a meeting early on Friday morning in Ann Arbor, but decided to check out the Conservatory directly afterwards. The temperature on the thermometer on my car dashboard read 13 deg F (-11 deg C). I entered into the main lobby of the Conservatory and gradually unbundled from my coat and other insulating layers. (They provide a handy coat room to stash winter accoutrements.)

As I opened to the door to the conservatory itself, I was greeted with a blast of warm humid air and the smell of green growing things. Towering green palms and bright color pops came into focus. It felt like entry into another world.

cacao pod closeup by PPJ (2017) CC By-SA 2.0

My body (and my soul, too) soaked in the surrounding warmth, humidity and lushness of the tropical biome section. However, I couldn’t resist long before taking out my cell phone to record images to tell the story.

Fluffy pink flowers by PPJ (2017) CC By-SA 2.0

My amateur smartphone photography expedition made it through the temperate and desert biomes before I finally ran out of battery.

For more images of my brief escape from winter (and the strange organisms that live there!), you can check out Protopian Pickle Jar’s Flickr Album Conservatory at Matthei Botanical Gardens.

World Soil Day – Dec. 5th

harvesting sweet potatoes in field
Harvesting Sweet Potatoes in Mechanicsville, VA. Lance Cheung, U.S. Department of Agriculture (2013) CC BY 2.0, on Flickr

In case you missed it, this past Monday, December 5th, was World Soil Day! Yay!

In this Onion piece, Scientists Make Discovery About World’s Silt Deposits But Understand If You Aren’t Interested In That. Similarly, you might gaze glassy-eyed at my exclamatory proclamation about soils, and move on to celebrity gossip or waffle recipes.

However, here at the Protopian Pickle Jar, I’m offering some reasons for blog-reading, clothes-wearing, oxygen-breathing, food-eating humans to get excited about soils!

Everything We Eat and Everything We Wear!
In TEVA, we taught the kids a chant: “Sun, Soil, Water, Air! Everything we eat and everything we wear!” Then, we challenged them to come up with an item that did not derive its existence from any of those things. (It’s rhyming version of the adage I learned in my undergrad earth science classes, “If it’s not grown, it’s mined.”) No matter what they came up with (plastic dinosaurs, fuzzy socks, water bottles) we were able to trace back its origin to a natural resource.

Every piece of clothing I’m wearing (including dyes, zippers, elastics and snaps)from my cotton underwear to my wool socks to my poly-blend shirt ultimately began with the soil. (Synthetics made from petroleum-based chemicals are mined from oil, which develops from long-dead marine algae, a kind of deposit of ancient solar energy.) Every item of food I eat – fruit, veggies, grains, meat, dairy, mineral supplements- began with the soil.* (Even food that comes from marine ecosystems is still linked to and dependent upon terrestrial soils.)

Ecosystem Services
While I was busy playing with the internet, earth’s soil bacteria are running the planet’s biogeochemical cycles. These soil-dwelling microbes are quietly moving the Earth’s carbon, nitrogen, oxygen, sulfur (and other elements!) through the biosphere using a series of metabolic handoffs. The bacteria may just be trying to get some energy (we might say, “Eat!”) by moving a few electrons around. Collectively, these reactions produce the atmosphere we breathe, the greenhouse gases and feedbacks that drive our habitable global climate, and fix the soil nutrients required for plants to photosynthesize.

One example of how microbes affect our environment : During the Biosphere 2 experiment, scientists sealed inside the closed environment faced incredibly low oxygen levels (dropping from ambient 21% to 14%). Barely able to breathe, the scientists could not sustain the daily activity required to continue the project. Biosphere 2 designers did not account for high levels of microbial respiration of the organic material in the Bio2 soils that were pulling oxygen out of the enclosed environment.

The Final Frontier
Not only do we rely on these soil microorganisms for the air we breathe and the food we eat, we don’t know very much about them. From the UN FAO Soil Portal: “Soil biology plays a vital role in determining many soil characteristics, yet, being a relatively new science, much remains unknown about soil biology and about how the nature of soil is affected.” We’re still learning how human activities affect soil microbes, often in unintended ways.

For more information, check out the Soil Science Society of America’s blog Soil Matters, Get the Scoop!


Regular readers of my blog may notice that I’m a little preoccupied with trash. Here on the Protopian Pickle Jar, I’ve been negotiating my relationship to all the Stuff in my life. Reducing and reusing get reframed as a moral component of consumption.  Composting becomes a personal virtue! Upcycling provides a creative outlet for the human-made objects I just can’t let go of.

Residential garbage trucks dumping a load in Savage, Minnesota, USA. At the landfill by Redwin Law (2007) CC by 2.0, on Flickr

I spend a lot of time thinking about trash. And then I found out that some people do it professionally! At the Discard Studies Blog, I got a glimpse into the work of academics examining the many different issues surrounding waste and waste disposal.
Thanks to the Discard Studies feed, I read a blurb posted on a new book, Waste Away by Joshua Reno, focused on the author’s experience working at a Metro Detroit landfill. Having recently moved to the area, I was curious about the massive landfills “rising like ziggurats from a flat glacial plain.” (I was particularly pleased with that metaphor.) Thanks to the magic of interlibrary loan, the folks at my local public library were able to source me a copy of the book. Twice. (Thanks MeLCat!)

Reno (now a Prof at SUNY Binghamton) was a grad student at the University of Michigan in anthropology, when he got a job at local landfill as part of field research for his dissertation. As part of his deal with his employer, he disguised the names and identifying features of the landfill and surrounding communities. So even if I don’t know the particulars (there are many large landfills in this area of western Wayne county), Reno’s descriptions of his work at a laborer at the landfill and communities impacted by it, offer a fascinating glimpse into a major local industry within a historical and cultural context. I especially enjoyed sifting through the local clues in the book to try to figure out what towns/landfills (or composites thereof) the author was *really* talking about.

I also learned the word “taphonomy,” the formative process by which an item (dinosaurs, shucked oyster shells, used plastic tableware) is buried and later discovered. It means slightly different things in the paleontology and discard studies subdisciplines. I am going to try to subtly sneak it into casual conversations whenever I can.

Edit (Dec 9, 2016): I found one!

The Onion, America’s Finest News Source, delves into taphonomy with their (satirical) article, Man’s Garbage To Have Much More Significant Effect On Planet Than He Will.

Tangents for this post:

Oscar the Grouch singing I Love Trash!

The Rule of Names

Pink slime
Wolf’s Milk Slime by Jason Hollinger, (2007) CC By 2.0, via Flickr.

In Ursula Le Guin’s Earthsea stories, knowing a person or animal or object’s “true name” gives a wizard power over him or her or it. Therefore, humans (and other sentient beings, like Dragons) take particular care to avoid sharing their true names with others, lest they be compelled by a power-hungry wizard.

I first learned about Linnean taxonomy, and the practice of classifying organisms by binomial nomenclature (e.g. Homo sapiens) in my middle school science classes. This was also about the same time I was reading the Earthsea books. Not surprisingly, these two concepts, The Rule of Names and the taxonomy of biological naming, remained linked in my mind for a long time.

field notebook sample
My field notebooks looked sort of like this. DG_1_023 Myristicaceae by Aber TREC, (2014) CC By-NC 2.0, on Flickr

In my field science courses in college, I was an omnivorous species identifier. Samples of Sonoran desert plants (well, the ones that would smush flat) made their way into my field notebooks, with carefully labeled common and scientific names.  With each new named species, it felt like I was slowly mastering control over my unfamiliar environment. If only I could learn all the names, I would know everything about the ecosystem.

When I got to TEVA, teaching environmental education, I was surprised that we were discouraged from telling kids an organism’s names (common or scientific) outright in response to the question, “What is that?”

Instead, of answering with “Oh, that’s an Eastern Hemlock (Tsuga canadensis,)” our training was to turn the question around to the kids.
“What do you notice about it? What about its color, smell, or texture can you describe?”

The best part was that kids would come up with their own names for plants based on their observations and continue to identify them for the rest of the time we were on the trail. For example, Eastern Hemlock became “Dragon Tree” (because of its large floppy wing-like branches and white-striped scales). It was only later that we told them the “real” names of the organisms, or let them look them up in a field guide by characteristics.

Striped white scales of “Dragon Tree.” Eastern Hemlock by Seabrooke Leckie, (2010) CC By-NC-ND 2.0, on Flickr

Some of my favorite names students came up with were Bubble Gum Slime (aka Lycogala epidedrum – a pink slime mold); Smurf Caps (aka Lactarius indigo – a mushroom that oozed blue goo); Ghost Roses (aka Monotropa uniflora – a flower-like bleached white plant); and Velcro balls (aka Arctium minus – burdock seedpods  covered with tiny hooks that snared hair and clothing.)

Had we told them the “real” name outright, the kids would have heard a name and promptly forgotten it.  Maybe even thought that the label encapsulated everything you could know about the organism. We would have missed a tremendous opportunity for kids’ exploration and engagement with the natural world.

Most recently, I get my nature fix by going on walks outdoors here in Michigan.  Sometimes, if I see something that I haven’t seen before,  (or that just looks really cool), I take out my cell phone and snap a picture with the camera.    I could (and often do) look up the species in a field guide.  I also started uploading my photos to the site iNaturalist, to source community identifications for my observations. By adding my photos, with dates and geographic data to the online database, it provides a record that other members can refer to. It’s a resource for researchers and a form of participatory citizen science.

I also have been learning to identify new species from the system, as well as tagging “Unknown” photos with high level identifications (i.e. “Plant” or “Fungi”) in order to make the photos more widely searchable to community members who can provide more detailed identifications. It’s a form of social media in some ways as addictive as Facebook or online dating sites (but instead of rating pictures of potential dates, I attach a label if I think it’s a vertebrate.) There is also definitely a serotonin hit when other members agree with your identification, or provide additional comments on an observation that is as potent as the “FB like” button.

I wonder (dubious seratonin hits aside), if I am I reverting to an earlier understanding of “Name *ALL* the things” vs. a more nuanced engagement and exploration of the natural world. Sure, the site has leaderboards to track which members have made the most identifications or posted the most observations. Is it a competition ala a birder’s Big Year or just creating a sense of order in a chaotic and messy world? And are either of these appropriate forms of interacting with nature? What about if they are tempered by the sense of wonder and Radical amazement that I feel on my walks, or looking at pictures of really, really cool organisms?

Beneath the Surface

Abstract by Andy Maguire (2016) CC By 2.0, on Flickr]
Abstract by Andy Maguire (2016) CC By 2.0, on Flickr

While I was watching the surface-bound shenanigans of other humans via Facebook, soil microbes have been steadily plugging away,  keeping the bio-geochemical cycles of the planet going.   A team led by scientists at the Lawrence Berkeley National Labs & UC Berkeley has reconstructed the genomes of 2500+ microbes that live in soil and groundwater of a Colorado aquifer. In addition to identifying (and naming) new phyla of bacteria, the researchers found new insights into how bacteria work together to power the carbon, nitrogen and other chemical cycles of the entire planet!

The paper appears online in Nature Communications. The soil microbiome census, using genomic techniques (“terabase-scale shotgun DNA sequencing”) to identify new taxa of bacteria in the samples, is especially important because while 1/5th of the Earth’s biomass exists underground, we still don’t know very much about about these organisms.

Once the genomes of the different bacteria were sequenced, scientists combed the data looking for genes related to microbial energy metabolism (gaining/losing electrons, carbon and nitrogen fixation, etc). By looking at which microbes with specific abilities were present in the samples, the researchers could infer what reactions (and combination of reactions) are taking place community-wide.

These combination of reactions are called “the metabolic handoffs.” Organisms may only have one or two metabolic tricks up their own sleeves (okay, I know microbes have neither hands nor sleeves, but bear with me here.) However, in the community of subterranean microbes, there are *a lot* of metabolic abilities across the different species. The waste products of one organism are food for another one that has the ability to extract energy from it. Or, as we liked to say as Teva Educators, “Waste equals food! Waste equals food! Waste equals food!”

TL;DR From the Press Release:

The scientists found the carbon, hydrogen, nitrogen, and sulfur cycles are all driven by metabolic handoffs that require an unexpectedly high degree of interdependence among microbes. The vast majority of microorganisms can’t fully reduce a compound on their own. It takes a team. There are also backup microbes ready to perform a handoff if first-string microbes are unavailable.

Previously unnoticed by humans, soil microbes are hard at work shuffling electrons as a team to keep the carbon, nitrogen, sulfur and hydrogen cycling around our biosphere. They deserve a shoutout from this grateful macro-organism.

Tangents for this Post:
Okay, I wasn’t just watching humans on FB. Other organisms include:
Glockenspiel-playing chickens
Rescued Cows
Pigeons (here and here)
Left-handed snail romance
Ticklish Rats