microbiology – In the Woods

sightings on another gloomy day

2.9.24 ~ North Carolina Botanical Garden

When we arrived at the botanical garden on Friday, Tim needed to tie his shoe, which gave me a minute to look at the roof of the gazebo he was sitting under. It was full of reindeer lichen and all kinds of moss so I took a few pictures with my zoom lens. When I got home I noticed those tiny red dots on the lichen. (above picture) Apparently these are called lichen fruiting bodies (apothecia) which contain spores that are dispersed in the wind. Just a little biology lesson for the day…

A quick stop by the bird feeders and there I found another life bird, this time a female Purple Finch!

The Purple Finch is the bird that Roger Tory Peterson famously described as a “sparrow dipped in raspberry juice.” For many of us, they’re irregular winter visitors to our feeders, although these chunky, big-beaked finches do breed in northern North America and the West Coast. Separating them from House Finches requires a careful look, but the reward is a delicately colored, cleaner version of that red finch. Look for them in forests, too, where you’re likely to hear their warbling song from the highest parts of the trees.
~ All About Birds website

We listened for a long time to a Carolina wren singing its heart out in the branches above us…

If we will be quiet and ready enough, we shall find compensation in every disappointment. If a shower drives us for shelter to the maple grove or the trailing branches of the pine, yet in their recesses with microscopic eye we discover some new wonder in the bark, or the leaves, or the fungi at our feet.
~ Henry David Thoreau
(Journal, September 23, 1838)

And finally, tucked away in a shady spot in the herb garden we found a patch of Lenten Roses blooming. They’re not actually roses, they are in the buttercup family. There are many varieties, flowers ranging in color from deep red to white and many shades in between.

It was a lovely surprise to find these flowers blooming so abundantly on a gloomy February morning!

salt marsh memories

7th Grade Class Trip
Mansfield Middle School (1969-70)
Barn Island Wildlife Management Area

Salt marshes have a long memory. Humans have a short one. Like sponges, salt marshes hold onto things. But for us, it’s out of sight, out of mind.
~ Tim Traver
(Sippewissett: Or, Life on a Salt Marsh)

4.12.23 ~ Barn Island Wildlife Management Area

Many years ago, my 7th grade class traveled for an hour-long ride to a field trip (48 miles away) on Barn Island on the Connecticut shoreline. Little did I know I would one day move down here to live in a neighboring town. It wasn’t until February of 2019, though, when my friend Janet suggested we take a winter walk here, that I got around to visiting it again. See: winter in the marsh. I took Tim there during the pandemic in December of 2020 when we were looking for isolated places to walk: See: reflections. So we decided to visit one last time before the big move. There is a very long path that crosses the marsh.

It was low tide and the water level in the tidal creeks was lower than it was on my other visits. I noticed a lot of clams and mussels in the exposed mud and clinging to the creek banks. The only waterbird we saw was a mallard but we encountered a lot of people and dogs, which was surprising mid-week. The woods beckoned from the other end of the path. Then we retraced our steps.

Barn Island is the largest and single most ecologically diverse coastal Wildlife Management Area in Connecticut. With over 60 years of continuous wetland research at this site, Barn Island provides a rare window into long-term marsh development both before and after restoration efforts. Its 1,024 acres are marked by centuries of cultural and biological history, once a vital resource for early colonial settlers and Native Americans and now for scientists and outdoorsmen. Its diverse habitats support rare plants and animals which add to its rich ecological resource base. Barn Island’s sprawling landscape sustains a wide variety of ecosystems and recreational activities; it consists of salt and brackish marshes, one of the state’s largest coastal forests, hilly uplands, intertidal flats, sandy beach, and a rare sea-level fen.
~ Long Island Sound Study website

The marsh is a microcosm of the world. With its peat meadows, meandering tidal creeks, microbes and mud, at the living, breathing edge of continent and ocean, it seems that life must have started here. Every microcomponent contributes to the whole. Discovering how this system works was a biogeochemical pursuit that took years and is ongoing.
~ Tim Traver
(Sippewissett: Or, Life on a Salt Marsh)

mussels and clams clinging to the tidal creek bank

In the above picture, looking south from the path, dock pilings can be seen in the distance. There is a boat landing there, on Little Narragansett Bay. We decided to drive down there and get a picture of the salt marsh from the dock. A solitary herring gull was quietly sunning himself on the dock when we arrived. He stayed put the whole time I was there.

The next picture is looking north to the salt marsh (between the woodlands) from the dock on Little Narragansett Bay. There are some people walking along the path that crosses the marsh, where we had taken our walk and had taken pictures. I zoomed in on them in the second picture, as much as possible.

On the way home we spotted two ospreys above a much smaller marsh near Paffard Woods, a preserve of the Avalonia Land Conservancy. We pulled over on the very busy road and tried my luck with the zoom lens. Unfortunately it was a very windy day and the car was shaking a lot.

We stopped again on the way home to pick up a cod loin for dinner and wondered what kind of fish we will find plentiful in North Carolina. Also, living by the sea it is breezy and windy here more often than it is calm. I started wondering what the wind will be like in our new inland home. And then we got back to our sorting and packing…

outbreak

“Cleaning Corpses During an Epidemic” by Fyodor Bronnikov

The other day I finished reading a riveting book, Spillover: Animal Infections & The Next Human Pandemic by David Quammen. A terrifying account of the recent history of disease scientists investigating bizarre and unheard of new diseases of animal origins, a thriller written by a gifted storyteller. Quammen explained the science so well in layman’s terms. This is one of those rare books I couldn’t put down. The fact that it was published eight years before our current worldwide coronavirus pandemic, a fair warning, makes it all the more pertinent.

Spillover is the process by which pathogens, hiding in wild animal reservoirs (also in factory farmed animals), travel into and infect the human population. But near the end of the book, after discussing the plagues of gyspy moths, which come and go, Quammen introduced the concept of outbreaks. We had a memorable outbreak of gypsy moths here in Connecticut in the 1980s so I could easily grasp the concept.

Ecologists have a label for such an event. They call it an outbreak.

This use of the word is more general than what’s meant by an outbreak of disease. You could think of disease outbreaks as a subset. Outbreak in the broader sense applies to any vast, sudden population increase by a single species. Such outbreaks occur among certain animals but not among others. Lemmings undergo outbreaks; river otters don’t. Some kinds of grasshopper do, some kinds of mouse, some kinds of starfish, whereas other kinds of grasshopper, mouse, and starfish do not. An outbreak of woodpeckers is unlikely. An outbreak of wolverines, unlikely. The insect order Lepidoptera (moths and butterflies) contains some notable outbreakers — not just tent caterpillars of several kinds but also gypsy moths, tussock moths, larch budmoths, and others.

We are prodigious, we are unprecedented. We are phenomenal. No other primate has ever weighed upon the planet to anything like this degree. In ecological terms, we are almost paradoxical: large-bodied and long-lived but grotesquely abundant. We are an outbreak.

And here’s the thing about outbreaks: They end. In some cases they end after many years, in other cases they end rather soon. In some cases they end gradually, in other cases they end with a crash. In certain cases, even, they end and recur and end again, as though following a regular schedule.

What could account for such sudden and recurrent collapses? One possible factor is infectious disease. It turns out that viruses, in particular, play that role among outbreak populations of forest insects.

~ David Quammen
(Spillover: Animal Infections & The Next Human Pandemic)

Chills have been running up and down my spine ever since I read the excerpts quoted above. We are an outbreak on this earth. Our population explosion can be fairly compared to an infestation of gyspy moths. Provocative thought, I know. But it’s humbling and sobering to appreciate that we are part the cycles of nature and while we like to think we can control our environment to some degree, when all is said and done, we know so little about the forces shaping our existence here on this little blue planet.

We now have 114 confirmed cases of COVID-19 in our town. Our county (New London) has 1,276 confirmed cases. Of those 7 are still in the hospital and 102 have lost their lives. Hospitalizations are way down here, which is encouraging, but we are still staying home due to our health risks. Please stay safe!

science is uncertainty

a man wearing a mask in 1918
image credit: Western Neighborhoods Project/OpenSFHistory

We all want answers today, and science is not going to give them. Science is uncertainty. And the pace of uncertainty reduction in science is way slower than the pace of a pandemic.
~ Brian Nosek
(The Washington Post, May 26, 2020)

I’ve been thinking about scientists a lot lately, beacuse of the pandemic, so when I read the above quote in the newspaper about “the pace of uncertainty reduction in science” it caught my attention. I remember my father teaching me that whenever science finds an “answer” it only brings more questions into focus. The more scientists learn, the more they appreciate how much they still don’t know.

Experiment, observe and gather data. Make educated guesses and investigate some more. My father spent his entire research career studying chicken viruses. It’s kind of astonishing that there could be so much to learn about just one kind of virus. Years and years of probing and analysis.

My father at work at the University of Connecticut,
sometime in the 1960s
~ photo by Thommie White, my grandmother

As far as I can tell, the scientists studying the coronavirus pandemic have been very candid about what they still don’t know. Yet, their best guess is that wearing a mask makes sense because it will likely protect other people from you if you happen to have the virus (with no symptoms) and are spreading it without realizing it. Combined with social distancing and frequent hand-washing, this is our best strategy for slowing down the spread of COVID-19 for now. Rest assured scientists are still searching for answers, hoping to reduce the uncertainty as soon as humanly possible!

varicella zoster virus

electron micrograph of a varicella virus
Public Health Image Library
Centers for Disease Control & Prevention

When our daughter Larisa was seven weeks old her two older brothers, ages 3 and 5, came down with chicken pox. This was before a vaccine for the disease was available. Not to worry, said their pediatrician. Because I was breast-feeding her my own immunity would protect her. But, a couple of days later, a few poxes appeared on her tiny little body.

The pediatrician examined her and scratched his head. He had never seen a case like this before. He said he couldn’t know for sure if this mild case of chicken pox would offer her immunity in the future. Years later, when Larisa was pregnant with Katherine, she was tested and did have chicken pox antibodies, removing any lingering uncertainty about her immunity.

But the story wasn’t over! Yesterday we got a phone call from Larisa who had just been to the doctor and had been diagnosed with shingles! Of all things! As far as I knew most people who get shingles are over 60 but she’s still in her 30s. And almost 8 months pregnant. But the doctor assures her that shingles poses no danger to the baby, even though chicken pox and shingles are caused by the same virus. (Chicken pox would have been dangerous.) Which tells me that they must have seen cases like hers before.

I haven’t posted in a while because first, I was very cranky about the relentless heat and humidity waves, and then, we were very busy with preparing for and traveling to Kentucky for our niece’s wedding and the family reunion immediately following. And now we’re getting ready to go down to North Carolina to help out. But I do have much to write about and hope to do so soon.

The good news is that autumn weather has finally arrived here and my mood is much improved!!! 🙂

helping hand

The first time I ever saw a print of this painting was at an estate sale, not long after my father died on September 19th in 2013. The expression on the man’s face reminded me of my father and the little girl reminded me of myself so I bought it. It’s not in the greatest condition and the coloring is way off. Perhaps the coloring on this digital copy is off, too. Some day I may replace it with a better copy.

He’s been gone for three years now and I still miss him, my favorite teacher. Papa taught me how to wash my hair, how to cross the street, how to trust my own instincts, how to treat animals, how to be compassionate and kind, how to swim, how to ice skate, how to paddle a canoe, how to chop an onion, how to look up words in a dictionary, how to do research, how to enjoy bird-watching, how to garden, how to walk (and play) in the woods — the list goes on. I think of him every time I do any of those things.

It’s almost autumn and I will be eating as many Macoun apples as I can while the season lasts. They were his favorites. He often told me the following story when I was growing up. (It first appeared almost 6 years ago on my blog!)

When my father was a boy growing up on a New England farm during the Great Depression, his family picked as many apples as they could and stored some of them in a barrel in the root cellar. Of course he ate as many as he could while picking them, but his parents had a rule about the ones in the barrel he found exasperating. If anyone wanted an apple later in the fall or winter, he was required to take one that was the least fresh. By the time they got to the fresher ones they had also become much less fresh! So all winter he was having to make do with eating not-so-great apples. If only he had known he might have called on Iduna to keep the apples fresher longer!
~ Barbara Rodgers
(Iduna: Keeper of Apples)

But perhaps I miss him the most whenever I hear a story on the news about a threat from a new virus or other infectious agent. Dad was a microbiologist and was utterly fascinated with microorganisms — viruses, bacteria, spirochetes, amoebas, fungi, parasites. He would never tire of explaining things about them to me and correcting any misinformation the media might be passing along to his fellow citizens. And I never tired of listening. I find myself wondering what he would have had to say about the Zika virus. It’s not easy finding someone so interested in this subject!

I didn’t notice it at first, but my father died on his older brother’s birthday. Jon Stephen was born on September 19th in 1909 in Ukraine. My father, Theodore William, never knew his older brother because Jon died of a ruptured appendix on March 15th in 1919 in New York, when he was only 9 years old. Papa was born three years later on March 13th in 1922. A little bit of synchronicity there I think.

Still missing you, my dear old Papa!