Literature Review: Dog Breeds

by Carl Strang

Part of my approach to natural history inquiry is to follow at least some of the scientific literature relevant to my interests. This is by no means necessary for hobby level inquiry. In my case it’s in part to feed my general curiosity, and in part force of habit established as a grad student and assistant professor of biology early in my career. Today I would like to review an article describing a paper that appeared in Nature this year by Bridgett M. vonHoldt and, as expected in a study of this magnitude, a long list of co-authors. The article I saw was here.

The group looked at a large number of nuclear genes in all major dog breeds and worldwide wolf populations. Wolves long have been known as the wild ancestors of dogs, but there has been some debate as to where their domestication occurred.

VonHoldt and company found a strong match to Middle Eastern wolves. An earlier study which pointed to an East Asian origin was based on a small segment of mitochondrial DNA, and so has less credibility. The oldest dog in the archeological record is 31,000 years, from Belgium. The oldest Middle Eastern find is 12,000 years old.

Comparing dog breeds, they found that relatively few genes account for differences in color, size and body proportions.

Focusing on their results for one oddly proportioned breed (and one I knew through Tag, the childhood pet in the above photo), I see that the dachshund is in a group with the basset hound, beagle and bloodhound. The closest (sister) group to them contains the spaniels. Here again I find a childhood connection through the first dog I knew, Timmy the springer spaniel.

The most distant group from these is composed of the basenji and husky-like dogs, which in turn are closest to wolves. Genetic dog groupings correspond well to established breed groupings (for instance those in kennel club dog shows) with exceptions, notably the toy dogs, which are smaller versions of diverse dogs scattered across the various kennel club groupings.

Going, Going…

by Carl Strang

It’s been a few weeks since I have provided an update on the demolition of the old friary at Mayslake Forest Preserve. Having removed the relatively narrow south wall, the contractors moved their crane into the courtyard, opened holes in the north and west portions of the building, then moved in tractors to clean out the insides and the roof.

The west wing soon was reduced to a framework of supports and floors.

At last a wrecking ball was brought into play, but not as I imagined from childhood cartoons. Instead of wildly swinging around, it simply was raised and lowered to smash and break up the concrete and rebar framework.

By two Fridays ago the west wing was history.

Attention has shifted to the east wing.

Meanwhile, concrete is being removed and holes are being filled around the periphery of the site.

Maple Leaf Miners, Canopy

by Carl Strang

On Saturday I returned to Maple Grove and Meacham Grove Forest Preserves to complete this year’s measurements of leaf miners in black and sugar maples. Earlier I reported the results for the understory. This time I was looking at fallen leaves to index leaf miner abundance in the forest as a whole. This can be regarded as a measure of these tiny caterpillars in the canopy, in part because the vast majority of leaves grow there and in part because saplings still are holding many of their leaves at this point in the season.

I went to 10 randomly selected points at each preserve and examined 30 leaves per point. The sunny, calm day was good for this as mines can be difficult to see after the fallen leaves have turned brown. I can hold the leaf so the sun shines on each surface, then hold it up so light shines through it.

In the five years that I have taken this measurement I have found few differences between canopy and understory leaf miner abundances. The most common difference is a lower incidence of Phyllonorycter tent mines in the canopy than in the understory, and such was the case this year at Maple Grove. Also at Maple Grove, Caloptilia boxfolds were less common in the canopy than in the understory this year.

All four genera of these tiny moths were in low numbers in the canopies of both preserves. The most abundant were Phyllonorycter at Maple Grove, where I found tent mines on 15 of 300 leaves, or 5%. That was the only species which produced a statistically significant difference between the preserves. In general, populations have been low since I began measuring canopy leaves, so I have yet to see a consistent pattern of differences. The only complete miss this year in understory and canopy combined was an absence of linear mines (probably produced by the non-native moth Stigmella aceris) at Meacham Grove (one turned up in the canopy sample there last year).

I have been interested in the effect of the more intensive management at Meacham Grove on insects and plants I am studying in these preserves. On Saturday I noticed that a burn had been attempted yet again at Meacham.

As you can see, the line of burning fuel dripped along the edge of the trail (which serves as a firebreak) did not take. There still is time for another attempt this fall.

Coots and Snow Buntings

by Carl Strang

On a brief trip to Culver, Indiana, last week I took some time to visit the town park and look for migrant ducks on Lake Maxinkuckee. There were coots aplenty, diving for water plants and quibbling as coots do.

There were thousands of coots, a few grebes and a loon, but no ducks other than local semi-domestic mallards.

The highlight came, not from waterfowl but from a trio of small birds that popped up along the shore of the lake.

Snow buntings! I never had seen one in all my childhood years of birding that town.

They were looking for seeds along the shore. It’s worth going out even on the dismal days of November. You never know what you may discover.

Winter Campfire 27

by Carl Strang

Last winter I posted a weekly series of chapters in a long essay about science and spirituality. I have been doing a little more reading and thinking in that area since then, and so before beginning this winter’s new series (a review of the prehistoric life and geology of northeast Illinois), I want to bring the last series up to date. This is the second and final new post in that series.

New Questions

In the previous post in this series I updated my thinking about the physiological nature of consciousness, its composition and its evolution. Other questions about physical reality arise from relativity theory. As I outlined last winter, relativity theory implies that all of space-time exists all at once, somehow, including us and our winding paths through it.

Gooddy points out that we navigate through space-time in our everyday lives. In that sense it is unremarkable. On the other hand when we, as people seeking to understand, create abstract notions of space-time, generalized and apart from our direct experience of it, we find this leads to conceptual challenges. If all of space-time exists all at once, how do we understand processes in that context? Processes such as evolution and consciousness seem to ratchet their way through space-time, frame by frame. How did this all come about, and do we truly have a part to play in shaping our own paths? If the future already exists, do our decisions really matter, or are we only deceiving ourselves? These are hard but important questions for which no one really has an answer. Foolishly, perhaps, I want answers and so put some effort into seeing how far I can go in getting ideas that feel right and give me guidance in living (and living with) my life.

For me, in my present understanding, I choose to think of time and space as building outward together from the singularity of the Big Bang. As far as I know, relativity allows for such a view. Once a local bit of space-time was/is built, it is eternal. In a sense we may be frozen in each eternal moment. However, each space-time moment has/had an origin, and in that origin I choose to believe that I, a space-time agent, had a creative role in determining the shape of what followed, through my choices and in my interactions within the holomovement or other components of the Universe. It all comes back to living each moment with the understanding that it counts for something, and our decisions matter because they produce the eternal shape of the Universe. And I find this conclusion satisfying because it seems to hold whether I come from a spiritual or a materialist starting point.

That said, we can function in our everyday lives as if time is real, just as we can act as though objects are solid and the space around us is as our senses inform us. It is only when we dive deep that we find such assumptions challenged and in need of deeper understanding. So, the seeking continues.

Black Oak, Maybe

by Carl Strang

Not being a botanist, primarily, I am inclined to miss plants unless I really focus on them. I count on their flowers or some other eye-catching feature to draw my attention. Such was the case last week with a particular oak in the north savanna at Mayslake Forest Preserve.

It doesn’t show so well in the above photo, but the leaves on the tree had turned yellow.

That is in contrast to the generally reddish and brown tones of the dominant white and bur oaks, as well as the bright red of the Hill’s oaks. I made my way to the tree, and found that its leaves were shaped like typical black oak leaves.

The lobes are shallow, unlike those of pin or Hill’s oak, and they don’t show the rhythmic size and shape of red oak lobes. The bark is consistent with black oak, though the tree is only a foot in diameter and so I can’t call that conclusive. The acorn caps are somewhere between those of black and Hill’s oak, though more like the former. For now I am calling it a black oak, though I think there’s a good chance that it’s a black/Hill’s hybrid. I am comforted by the fact that even botanists struggle with the oaks.

What’s with the Crows?

by Carl Strang

Ever since the arrival of West Nile virus several years ago I have grown accustomed to seeing few crows in DuPage County. Urban and suburban areas supply plenty of habitat for the species of mosquitoes that most often carry the virus, as opposed to rural areas, which do not. Consequently I have come to think of the suburbs as a population sink for crows. The mosquitoes carry death to crows in the late summer. New crows appear in the winter or spring, apparently having immigrated from rural areas. Some of these may nest, though most apparently are young birds not quite ready to do so. Thanks to the virus, they don’t get a chance.

This fall has been different. I am seeing crows regularly. The most remarkable case came on one of the very windy days we experienced last week (cue wind shot).

As I stopped by forest preserve district headquarters in the afternoon, I saw a flock of at least 30 crows. They perched on the HQ roof, but spread out before I could get the camera untangled.

A few remained on the roof.

Others went to the lawn, or to nearby trees.

I was away from the county for most of the crow nesting season, so now I am asking myself: are these locally raised birds? Have they at last evolved a resistance to the virus to match that in our other avian species? Can we look forward again to easily finding great horned owls?

Winter Campfire 26

by Carl Strang

Last winter I posted a weekly series of chapters in a long essay about science and spirituality. I have been doing a little more reading and thinking in that area since then, and so before beginning this winter’s new series (a review of the prehistoric life and geology of northeast Illinois), I want to bring the last series up to date with two additional posts.

The Evolution of Consciousness

The main scientific questions left suspended at the end of that series revolved around the nature of consciousness and the meaning of process (a time-dependent concept) in a relativistic Universe. By “consciousness” here I am referring to a limited sense of that word, i.e., the experience of the specious present. Here again I am borrowing from Lockwood’s review of physiological studies. Our experience of the present moment is a roughly half-second span of time (the specious present) in which we take in sensory impressions, have access to memories of the past and can imagine or plan our future actions. That half-second is composed of 15-20 frames, each around 30 milliseconds long. As each new frame comes into our perception, one drops off the back. Our sense of the passage of time is the result of a given frame passing its way from front to back through the specious present.

My starting point for the next step in this study was the following question. Shouldn’t there be disorders that help us to understand the mechanism by which consciousness spans time and isolates it? The inspiration for this possibility comes from developmental biology. Mutations that cause bizarre physical features in fruit flies, for instance an extra leg in place of an antenna, provide the opportunity for the geneticist to understand how the fly’s body is produced from the genetic instructions within its starting cell, the fertilized egg. Examination of such processes from an evolutionary standpoint provides insights into evolutionary processes and history (the powerful new science of evo-devo). By analogy, then, it seemed to me that neurological disorders might cast light on the physiology of consciousness. This led me to the book Time and the Nervous System, by British neurologist William Gooddy.

Gooddy points out that all of our experience is produced by our nervous system. I discussed this myself early in the Winter Campfire series when I focused on what sensory impressions really are. Gooddy expands this notion to all of experience, including time. Abstractions such as a separate world of three-dimensional space through which we move in time are constructs. We create that world. In fact we live our everyday lives as navigators of space-time.

I was especially interested in what Gooddy had to say about time-related disorders. Here’s an extended quote:

“An example may be provided from patients with Parkinson’s Disease in which (because of loss of brain cells) there is a marked stiffness, with slowing of voluntary movements, usually associated with some degree of tremor. The observer notes how ‘slowed down’ the patient is, with even simple tasks taking such a long while that it may be quicker to offer help. But if the normal observer suggests that, ‘everything is very much slowed down’, and, ‘the time must go very slowly for you’, the patient will say, ‘It is just the opposite. My own movements are much slower than they used to be but they often still seem normal unless I see how long they take by looking at a clock. The clock on the wall of the ward seems to be going exceptionally fast, not slow, probably because I now can get much less done by clock time than I used to’.”

Gooddy lists and describes eight categories of space-time-related disorders. These include loss of memory, loss of an ability to plan or project oneself into the future, the scrambling of sequences, and loss of the ability to navigate in space, as well as changes in the rate at which time passes subjectively as described in the previous paragraph.

These evidences seem to break our experience of time and consciousness into three parts: memory, the specious present, and imagination or the projection of oneself and one’s actions into the future. Amnesia removes the past from experience. A person who has lost both the past and the ability to imagine the future is living entirely in the present moment. While living in the moment by choice is an important aspect and goal of spiritual experience, people stuck in that state no longer can take care of themselves. Lacking memory, the benefit they gain from living in the moment is limited.

Given that these three elements can vary, more or less independently of one another, as a biologist my next question is: how did evolution arrive at the common pattern? What determines the number of frames and their duration in the specious present? Why not expand to, say, an hour’s worth, either by lengthening the frames or by increasing the number of them held in mind at once?

Those questions lead to the following thought experiment. I imagine early life, when animals first were acquiring the ability to move. Movement itself would allow an animal to go to food rather than passively waiting for it to drift by as in the previously dominant filter-feeding mode. The ability to move also made it possible for early animals to escape an approaching hazard. Such a hazard would have to be perceived to be avoided, and such perception would require the animal to possess an early form of the specious present so that the hazard’s speed and trajectory could be assessed. The selective advantage accruing from all the little mutational steps along the way would, over time, produce this result. Falling objects or approaching predators perhaps would require a fast reaction that would be impeded if too many frames were being processed by consciousness or if the frames were too long in duration. The big push would have been the evolution of predation, which would bring hazards more frequently than would accidents. As prey evolved the ability to evade, predators would have to keep pace by increasing the speed of passage of their own specious present. The length of the specious present, in this thought experiment, is limited by the animal’s ability to process information. The frames would have to be short to allow an effective assessment and response. The number of frames couldn’t be too many or their analysis would slow down the response time detrimentally.

Lockwood discusses athletes’ flow (the sense that events have slowed down; this also happens in times of physical danger and crisis) as perhaps being a reduction in the number of frames in the specious present, allowing faster processing but experienced as a slowing of time. This supports some limitation in the nervous system’s processing ability being the major constraint on the length of the specious present.

Returning to the evolution of consciousness, I can see how memory would be an advantageous addition, allowing the animal to take advantage of experience. Projection into the future allows for the avoidance of hazards. All of this implies that any animal that displays these capacities has to be regarded as possessing consciousness. An important caveat is that instinct could substitute for memory and future projection in some cases.

This discussion hasn’t had much to say about spirituality. Mystical experience is part of the input we can receive. Our consciousness and memory can take in and store such experience, but how it comes to us remains unresolved.

That is where my question about time-and-space pathologies has taken me. I’ll need one more post in this series, for now, to recast some remaining questions.

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