Another naturalist, more yards

 kw: book reviews, nonfiction, science, biology, naturalists, natural history, citizen science, cities

When you think of Picnic Guests, what do you imagine? This image probably doesn't come to mind. Ants are the more likely thought. The third chapter of Secret Life of the City: How Nature Thrives in the Urban Wild, by Hanna Bjørgaas (or the fourth if you count a long "Introduction") considers ants. Ants that invade the author's city apartment, ants that drive her to consider chemical warfare. Discussions with a couple of scientists dissuade her, and she simply pays more attention to keeping things clean and outwaits them.

In the meantime, she uses a magnifier to get a closer look at one. At 20X, it looks quite fearsome. Ants are well fitted for living in a great many environments. They may be the primary ubiquitous animals. They live on six of the seven continents; none are native to Antarctica (the only insects that live there, in a few coastal areas, are a couple of species of midges that can survive being frozen for half the year). They abound everywhere else, and probably outweigh the sum of all mammals, humans included.

Ms Bjørgaas lives in Oslo, Norway. Her book was translated from Norwegian by Matt Bagguley. The nine titled chapters touch on living things she paid attention to during nine months of the year. She begins the year with crows, the most intelligent birds most of us are likely to encounter. Crows in the city, like many types of city birds, are less skittish around humans than their more rural cousins. They may not be as human-adapted as pigeons—sometimes you almost have to step on a pigeon before it flutters away—but they seem to have a keen sense of how far you can reach, should you be so inclined.

In the Introduction, though, which takes place in Antarctica where she worked briefly as a tour guide, her focus is not so much on penguins as on a particular species of lichen that caught her eye. Both crows and lichens appear later in the book also. The November chapter focuses on lichens, and is titled, "The Written Language of the City." This is because, among the great variety of lichen species, some are more sensitive, and others more tolerant of the polluted air of cities, particular when it includes sulfurous (stinky) gases. 

This picture shows at least three species of lichen on an old branch, in an area with rather clean air. Using citizen scientists to help collect observations, researchers have developed a "lichen scale" to measure the level of air pollution in and around cities. One may then map concentric rings that surround sources of more egregious stenches such as paper plants (Sixty years ago I remember the smell of paper plants near Newark NJ, which my cousin called "the armpit of New Jersey". It's been cleaned up a bit since then).

The author did an experiment in soil fertility. She bought nine pieces of cotton underwear and selected three locations, one in a desiccated city lot, one in a park, and one well outside the city in the forest. In each, she dug three holes and buried a garment a spade-length deep in each hole. Months later, there was nearly nothing left of her "offerings" in the forest, and the parkland holes yielded semi-composted cloth bits. The third location had been paved over since, which demolished that part of the experiment. I expect that the cloth may have been darkened a bit, but would have been otherwise almost unchanged, and I suspect she would agree. That's what others have found.

If you find the spectacle of a woman digging holes in a city park amusing, consider coming across her prone upon the ground, examining the contents of a shallow scrape with a strong magnifier. She did a little of this, as she tells in "August: Stories from Underground". With a bit more discretion, she visited a soil scientist, who showed her the life beneath our feet with a video microscope. A tiny springtail (the size of a comma) was a hideous monster compared to protozoa and other small denizens of the soil. And, of course, it must be said that the number of bacteria in a teaspoonful of soil will typically exceed the entire human population of the earth, perhaps ten times over. Even the dry, sandy soil of a trampled path in a city may contain a billion bacteria per gram.

This book is a delightful contrast to nature books that tend to concentrate on, for example, birds, or beetles, or some other focus. There is room in the concept of "naturalist" for anything living. I wish the book had an index. Still, it is fascinating and it opens one up to some of the variety to be found in any environment, if we will simply slow down and look, and listen, and observe.

The naturalist in the yard

 kw: book reviews, nonfiction, science, biology, naturalists, natural history, citizen science

I took this picture in 2010, the first year I participated in the Great Sunflower Project. It is a sweat bee of a species common in the mid-Atlantic area, gathering pollen from a Lemon Queen Sunflower, the flower designated in the Project for attracting pollinators, primarily native bees. For those who like to be involved with natural history in their own surroundings, GSP is one program that Thor Hanson recommends in Close to Home: The Wonders of Nature Just Outside Your Door.

According to directions, I planted sunflower seeds in early spring, and once the flowers began to bloom, I stood nearby for 15-30 minutes a few times weekly to record what I saw. The project organizers don't expect us backyard naturalists to identify the species of every bee. They supply a simple field guide to several broad types of common bees, and participants report how many of each type appears during each session of watching.

That year I saw very few honeybees, at least in the late summer when the sunflowers were blooming. But as summer cooled toward autumn, I saw a few more, not just on the sunflowers, including this one on a flower of garlic chive, near a smaller bee that I don't recognize (it is near upper left).

I participated in the project for several years, then stopped. Standing around on a hot August day is rather hard on me. But we have plenty of fare for pollinators in all seasons, as seen in the pair of pictures below:

On the left, three tiny bees (about 8mm) are picking over Sedum flowers that bloom in the spring next to our front walk. Oh the right is a flower bed with flowers for all seasons. A Hellebore is almost hidden beneath late-spring-blooming evening primroses. The Hellebore blooms from February until June. We have a few in other parts of the yard, to keep pollinators supplied while they await other kinds of flowers. In mid-June the Echinacea begin to bloom, and carry on for a month. Lavender and heather flower later, and several other flowering plants push the season almost to first snow. This garden is next to a crabapple tree, that flowers in mid-spring, and across the yard, an apple tree flowers in early spring.

One more creature we recently began to try to attract is the Monarch butterfly, with these milkweed plants. There is a schoolyard nearby that has a big patch of milkweed, but this is just the third year for us. We started with a single plant we grew from seeds we collected in the schoolyard. So far we haven't seen any butterflies, but these plants attract many more honeybees than I've seen in ten years or more. They also become infested with milkweed bugs. When they are very small, the little red nymphs must have honeydew like aphids do, because ants tend them.

Early in the book, Thor Hanson uses the term "backyard biology." Later he says it might be better to speak of "yard biology," though it is less euphonious, because nature doesn't just hide out behind our houses. It is all around us. The ten chapters (plus an Introduction and Conclusion) reveal the manifold riches of his own yard. Of course, he does live on an island in Washington state, with a yard that's bigger than average…multiple yards, from the sound of it. However, any of us, if we're willing to slow down and observe, can see a lot.

Thinking it over, we can gather quite a list of the variables that lead to quite a variety of creatures making themselves at home in any yard: variations of light and shade; warmth on cooler days and shelter on hotter days; foods that appeal to this or that sort of creature; shelter for the shy ones (such as little songbirds) and open spaces for the bold (rabbits, squirrels, and foxes; even deer when apples are falling).

I tend to favor insects because many of them ignore humans if we move gently and don't breathe on them. They're easier to photograph than birds. One acquaintance of the author uses a lighted sheet at night to attract moths, which he photographs obsessively. He has catalogued hundreds of species in his yard. One can do the same for beetles; many will also come to a lighted sheet. The beauty of a light trap is you don't have to catch and kill to identify most species (sometimes it's necessary, though).

Dr. Hanson speaks much of birds, and advises getting not just "a birdhouse" but a dozen or more, of various sizes, because there are many varieties of bird that prefer to nest in cavities. There just aren't enough abandoned woodpecker holes to go around. During my last few years at my company I was on a team that monitored birdhouses scattered around the property. All were sized for bluebirds, which also made them ideal for swallows (2 species), wrens (3 species) and chickadees. On occasion we would find a birdhouse in a more sheltered location that had been taken over by a pair of starlings, which are rather large; they had pecked the hole a lot bigger. At the end of the season we would take that birdhouse to the company shop to be fitted with a new door, this time with a metal collar in the hole! On another part of the property there were much larger boxes designed for wood ducks. My wife and I have talked it over a little. We may get (or make) a few birdhouses.

Another project recommended in the book is iNaturalist. It is a phone app, with an accompanying website, where I find it helpful when I want to edit an entry. TIP: The GPS on my phone is not as accurate as I'd like, so I go into the website later and edit the location if it is too far off. The minimum "native" accuracy of an iNaturalist geolocation is four meters. That's usually sufficient; for us Yanks, that comes to a radius of 13 feet. On the website, if you remember accurately where you were (it shows you a detailed aerial photo), you can enter a value as small as one meter.

Here I have focused on the "what we can do" suggestions. The book is also chock full of stories about various animals of all sizes found in the author's yard, or discussed by his friends and colleagues. Getting closer to what goes on outdoors is good for us. We need to slow down and, typically, just look and listen. It is good to recognize that we are part of nature.

Spiders continue to spread

 kw: blogs, blogging, spider scanning

After a week of lower activity, scanning of this blog has leapt up again in the past two days. Here's the list of actors for the past 24 hours (as of ~4pm Tue, 6/10/25):

I haven't seen the US drop to 12th place before. The heavy hitters today are Vietnam and Brazil, but nine other rather unexpected countries followed, above the US. I surmise that today, and recent heavy activity cycles in general, are driven by AI training. Good luck, folks; this blog is rather specialized.

Poorly-known life in the largest habitat

 kw: book reviews, nonfiction, science, oceanography, marine biology

The Blue Sea Dragon is a beautiful creature, a type of sea slug. You wouldn't want to handle one, in spite of their tiny size, around 3 cm at most (1¼"). They are armed with stinging cells similar to those of the Portuguese Man of War, which they obtain by eating small animals related to the Man of War and "appropriating" their stingers!

They are rather rare, found at or near the surface of warm oceans. This Wikipedia article has much more about them. They are also described on pages 147-148 of Into the Great Wide Ocean: Life in the Least Known Habitat on Earth by Sönke Johnsen, where they are presented as an example of small pelagic animals that avoid being eaten by being, not just noxious, but venomous. Sea slugs in general are tasty treats for many oceanic predators. Not these!

"Pelagic" is from a classical Greek word meaning "of the open ocean." By definition the pelagic zone is nearly all of the world ocean, all of the salt water that is far enough from the coast to be unaffected by surf action and is also above the bottom (by a rather poorly defined distance; at least several meters). The upper kilometer of this is of special interest to Dr. Johnsen, being the zone in which at least a little sunlight penetrates, making photosynthesis possible, and also making sight hunting possible.

The book is part memoir, part travelogue, and part catalogue, a catalogue of the attributes needed by the animals that live in the upper pelagic zone, never approaching land or the sea bottom…at least not voluntarily. The book is illustrated by Marlin Peterson; his depiction of the sea dragon, Glaucus atlanticus, is shown here for comparison with the photo above.

To study pelagic creatures is costly and difficult. Operating an oceangoing ship costs thousands of dollars daily, and the extra crew needed to handle a submersible or an ROV, or both, must be paid, and such equipment is worth millions. So, a dozen scientists and a couple of dozen crew may spend half a month of a month at sea, and get a smattering of photos via the ROV or in a submersible, but sometimes they return without sighting anything at all!

A large majority of pelagic animals avoid being seen by being transparent. The author writes of being on "blue water" SCUBA dives, knowing that thousands of finger-sized salps are all around, and seeing nothing. Animals that are not transparent are typically counter-shaded, and those that reside a little deeper down, where there is no upward-welling light to reflect off a silvery ventral side, have arrays of controllable bioluminescent organs that make their underside match the light coming from above. The "arms race" between predators that don't want prey to see them, and prey that don't want predators to see them, makes them hard to detect, even by each other! Thus, many can also shine their own bioluminescent flashlights to find a mate, for example, at the risk of attracting a predator.

Past knowledge of mid-oceanic life was gathered by trawling. One may thus learn of the existence of numerous animals, at least the slower ones. Not many oceanic squid, for example, are brought up by trawling. The fragile beings caught in a trawl usually arrive as clumps of unidentifiable sludge. By analogy, imagine studying London by dragging an anchor on a chain from a fast dirigible, to try to learn how the British live. More useful and appropriate methods are continually being devised.

An interesting contrast is presented in a section on Navigation. A pair of scientists the author knows uses a large, boxy tank surrounded by electromagnets to test juvenile sea turtles. They appear to have a magnetic sense, which helps the females navigate to their favored beach for laying their eggs, for example. Now consider elephant seals. The females come ashore to meet their mates, give birth, mate again a month later, then head out to sea. It is known that they travel thousands of kilometers to good feeding grounds, then return to land to give birth. It is also known that they swim a couple of hundred feet down (50-80 meters), so they can't be navigating by the stars. But a female elephant seal weighs a ton, and though she is less fearsome than her four-ton mate, she is still more dangerous than the average lion. You aren't going to get one of these in a magnet-bounded tank! As the author writes, with better-than-average scientific humility, he and others have studied elephant seal navigation for several years, and so far have learned nothing!

Such studies would be so much simpler if these animals—at least the smaller ones—could be brought into the laboratory and "put through their paces." But animals in the lab may not exhibit any of their in-the-wild behaviors, and the things they might do in a tank are likely to bear no resemblance to what they do in the open ocean. Scientists labor to devise more clever and less intrusive instruments, hoping to observe natural and normal behavior. Really, the study of this immense habitat, that covers 70% of the surface of the Earth, has just begun.

Artificial aliens?

 kw: book reviews, nonfiction, science, biology, physics, cosmology, genetics, first contact

To put Sara Imari Walker's last question first, will first contact with a true alien occur in a laboratory? Dr. Walker's book Life as No One Knows It: The Physics of Life's Emergence is a heady brew of ideas. She has a wonderful kind of mind that looks at things from angles others would never imagine existed, and she has managed to find a number of kindred souls with a similar talent.

Dr. Walker and her colleagues propose Assembly Theory, a new view of evolution in which technology has become an agent of evolutionary change, and "selection" takes on a meaning that would mightily bemuse Darwin. Her explanations make sense. I don't yet understand enough about assembly theory to attempt an explanation. I must content myself with a few bullet points gleaned from the third chapter ("Life is what?"; intended to be pronounced with a distinct upward lilt, as, "Life is WHAT??"). These items do not describe life, but rather objects. Objects as the new theory envisions them:

• Objects are finite and distinguishable
• Objects are breakable (I would have said, "can be disassembled")
• Objects exist more than once
• Objects are lineages
• Objects form via selection

Some objects are living things. Some are not. A wooden table of the kind I built long ago to hold my mouse pad next to my desk is an example. I constructed it using nine pieces of wood, eight large wood screws, 24 small nails, and some glue. The top is plywood, which itself was fabricated by someone else before I bought it from a lumberyard and cut it to size. We can inventory the statements. 

• My little mouse-pad table is finite (less than a meter tall) and is distinct from other items of furniture in this room, some purchased (and thus built by someone else) and others built here, by me.
• It can be taken apart, by removing the fasteners and breaking the glue joints (no doubt tearing wood in the process). I don't plan to do so.
• I have made other similar tables, which I suppose qualifies at "exists more than once." Worldwide, there are many tables of many designs, but all related in general shape and function.
• Is it a lineage? The idea of "table", generalized from "supporting platform" is certainly a lineage, going back to the first table or table-like platform built by a human or prehuman creature.
• "Selection" in such a case means that the I selected to make a table rather than a cantilevered shelf hung off my desk, or other possible means of supporting my mouse pad.

Consider a screwdriver. The author writes, "An evolutionary chain of objects is necessary to assemble screwdrivers into existence." In other words, the forebears of screwdrivers include machine shops, mining and metals productions facilities, and creatures like us to think them up. In the case of living things, the "lineage" of everything alive today goes back about 3.9 billion years. All known life comes from life. What came before?

This is the crux of the matter for assembly theory. The theorists use these concepts to imagine life as we don't know it, life as no one knows it.

Side question: Can objects be produced by other objects that are not living? They can, which is apparently where all nonliving and never-previously-living things arose. For example, a planet such as Earth was assembled from dust, rocks, etc., under the influence of gravity and electromagnetism and sundry other possible forces. Also, natural, nonliving actions produce raindrops and snowflakes in clouds, sand and gravel from rocks, and so forth. 

However, the production of objects by nonliving processes yields objects with very few unique parts. Living objects tend to be much more complex, as do many of their products. Thus this conjecture, stated at least a couple of times in the book, "Life is the only thing in the universe that can make objects with many unique parts." The author notes that many kinds of minerals don't form in the absence of life. I recall taking a class in minerology, in which the professor stated, "There are about 1,000 mineral species known in the earliest rocks, before there was much life on Earth. There are now more than 4,000 minerals, and most of them can only form because there is life on Earth." Today the number of catalogued minerals is almost 7,000, and that may grow to more than 10,000 as busy geologists keep finding new stuff.

This principle yields the basis of the author's "assembly index", a measure of the minimum number of steps needed to produce an object. This gets us away from looking for life that is too chemically similar to "Earthlings" (from microbes and viruses to whales and forests, with us in the mid-range). If the assembly index of numerous objects collected on an exoplanet is large enough, we could conclude that life most likely produced them. The critical number is, according to the author, fifteen.

Frankly, I don't know how assembly index is calculated. I read that the assembly index of the molecule ATP is fifteen. This molecule has 47 atoms. Perhaps the calculation allows the synthesis to begin with smaller molecules that natural processes have already produced: water, carbon dioxide, ammonia, phosphorus oxide, and perhaps even small hydrocarbons such as ethane (ethane can result from abiotic, or nonliving, processes, but in the presence of a living biosphere we never observe it).

Therefore, the number 15 seems to be a good "filter" to discern objects produced by life.

A second prong in the approach by proponents of assembly theory is the development of a "chemputer", a semi-automated way to sort of "3d print" molecules, designed to have certain properties, in an attempt to produce a chemical system that takes on the attributes of life: reproduction, ingestion of supplies, elimination of wastes, relationships (very broadly construed), for example. Were such an effort to succeed, using large numbers of chemputers to explore the "assembly space" of small-to-medium sized molecules, there might indeed be alien life produced in the laboratory. It would be as alien as anything we might find on a planet far away, perhaps even more so. 

The key to grasping assembly theory is the claim that all things life can build are historically contingent. We can see this in the visible relatedness between the wide range of animals known as "tetrapods". They all have four limbs. The mythical flying horse Pegasus cannot evolve from a horse, because to do so would require adding two new limbs (to become wings) to a body that already works well with four limbs. The intermediate steps required don't make sense (and let's ignore the physics of wings long enough to support a half-ton animal). In fact, mammalian hexapods in general aren't likely to arise, because the competition from extremely well-adapted tetrapods has already pretty much filled all available ecological niches for critters bigger than a cockroach…on land, at least.

Historical contingency is a key concept. Finger-and-toenails didn't evolve all at once. They descended from claws. Claws came from something else. All living things trace back to a single-celled creature called LUCA, the Last Universal Common Ancestor. LUCA may not be the first cell. At one time other living things could have existed alongside LUCA that may have had quite different chemistry and cellular mechanisms. But only LUCA has descendants: us, and every living thing in the biosphere of Earth.

Our chain of imagined forebears stops with LUCA. Our knowledge is further constrained, because it is extremely unlikely that any creature now living is descended without change from LUCA. When I say "extremely unlikely", that middle E needs to be drawn out, "Extreeeeeeeeeeeemely!" Meaning, utterly impossible unless the universe is truly infinite, with an infinite number, not just of planets, but of biospheres. Even if we somehow track back the chain of biochemical contingency to "show" us a robust model of LUCA, the chain stops there.

I like the idea of the chemputer. But I don't hold out much hope. The assembly space of "small molecules" is too big. For example, if we "restrict" ourselves to the twenty most common elements, all of which are found in known life, and all of which are likely to be in any possible kind of life, and further, we call a molecule "small" if it has fifty or fewer atoms (just a tad bigger than ATP), the number of possible chemical species (most of them quite chemically unstable) is close to ten-to-the-power-of-65. A 66-digit integer. How large is that number? The number of stars in the visible universe is thought to be a 22- or 23-digit number. Could the average number of planets be as great as ten? Even if that were so, the number of planets in all the galaxies in the visible universe is no larger than the largest 24-digit number. It is hard to think about 66-digit numbers in any useful way. 

Dr. Walker dreams of being the researcher in the cartoon above, "meeting" the first true alien in the laboratory. I hope her dream comes true. But I think it more likely that we'll come across something, somewhere, soon, that proves life as we don't yet know it does in fact exist.