Monday, October 31, 2016



Of the many environments on earth, freshwater streams are one I have studied the most.  We tend to automatically judge an environment in terms of its expected natural state before civilization arrived.  But erosion of sediments and their deposition are not always something we would include in our ideal stream even though it has been part of stream development forever.  The different sediments of a stream provide homes for different organisms based on particle sizes from silt to bare rock, reflecting water velocity, and other organisms; the assortment is affected by those factors as well as temperature, light, water chemistry and perhaps other interactions.

Just looking at a stream, pond, or lake and determining the gross aspects like water clarity, plants, and animals present may give an approximation of the water quality and its ability to sustain life.  Measurement of chemical and physical features of the water along with a more precise inventory of plants and animals present can tell more about present and past conditions of the water.

Dissolved oxygen is often the most significant indicator of water quality in terms of ability to sustain a diversity of fish, invertebrate, and plant life.  Chemical testing to determine dissolved oxygen can show the oxygen level present at the time of testing.  But a shallow body of water with high density of plants could show depressed oxygen levels or even no oxygen at dawn and supersaturated oxygen levels in the early afternoon on a sunny day.   

In a stream, presence of several species of case-building caddisflies and/or stoneflies shows good oxygen levels are maintained because they need it to survive because their “gills” are out of the main flow of water passing the insect.  Conversely, an abundance of fly larvae, especially rat-tailed maggots, generally indicates organic pollution depressing oxygen levels; they survive because they may extend their “tail” to the surface and breathe air.  Like insects in general, most aquatic insects have air filled trachea that extend throughout the body, but during their immature aquatic phase the trachea do not terminate at surface spiracles but do extend into the “gills”.

If the organic food wastes in the water are not excessive, oxygen used by fish and other aquatic life can be replaced by plants releasing oxygen produced by photosynthesis, and by diffusion from air at the water surface.  The surface input can be a major source in small turbulent mountain streams.  When dissolved and/or particulate organic material is excessive, bacteria are a major user of oxygen; anaerobic bacteria can continue the breakdown of organic matter when oxygen is depleted and in the process release methane and other even less desirable by-products of anaerobic respiration.

When excessive organic pollution enters a stream at a specific location, the downstream portion will rapidly decline in dissolved oxygen and most higher organisms. If excessive pollution loads are not entering downstream the stream will gradually recover if toxic residues are not part of the load.  Toxic materials, if part of the pollution load, can accumulate in stream sediments and be gradually released as they further complicate recovery of a polluted stream. 

In a lake or pond, a one-time input of organic waste will over time have a recovery time sequence much as is encountered in the downstream sequence in a polluted stream; the recovery time may be slowed as compared to a stream because of the lack of turbulence.

A biotic index of water quality can be determined from a survey of the organisms that are present.  Since we know the requirements of most organisms they can be used to define the water quality in a general way.

Good water quality is often associated with a variety of fish and other vertebrate life, aquatic insects, crustaceans, shelled mollusks, flatworms, annelids, diatoms and green algae, and vascular plants.  Water clarity may allow one to see the bottom in water up to several meters in depth.

Reduced water quality will result in an absence or reduction of the variety of the above groups, perhaps an excess number of some that are more tolerant and an increase in blue green algae both in the water and attached to solid structures.  Visibility of objects below the surface is very limited.

Severely polluted water will have no fish, mammals, reptiles, amphibians, and few of other groups.  Some fly larvae and tubificid worms may be present or abundant in shallow sediments, as well as a coating of “sewage fungus” on submerged objects.  Some emergent plants rooted in shallow sediments may be present.  Water may be nearly opaque.

Toxic substances may result in the death of all organisms and give little visible evidence of their presence.  Mine drainage in mountain streams may acidify the water and prevent aquatic life without being very obvious.  PCB’s in paper mill effluents from efforts to recycle certain types of paper resulted in loss of all visible bottom life in a stream that previously had some when it was severely polluted by normal paper mill wastes.

Toxic substances may have killed off some or all of the organisms as they pass downstream so a test of the water may not identify the toxic material.  Residues may be in the sediments and/or retained in dead or living aquatic organisms present.  An upstream search may help localize a pollutant source if the junction with normal stream inhabitants is reached.   A localized source of a pollutant is referred to as a point source, more generalized sources include surface water runoff, atmospheric fallout, and sometimes groundwater discharge from seepage or springs may also include contaminants.

Surface water runoff containing excess phosphorus and insecticides is often worse from city lawns than from agricultural fields.  City dwellers often think if a little bit of chemical fertilizer or insecticide is good, more is better.  Farmers know better, it is a waste of money to apply more than is needed to do the job.  Many communities now have hazardous waste disposal facilities to reduce contaminants that cannot readily be removed by standard sewage treatment; otherwise a greater variety of toxic on other noxious substances reach our streams, lakes, groundwater, and oceans.

A polluted atmosphere, like the one resulting from the asteroid that killed the dinosaurs, is unlikely to occur in our time.  That is especially so since we now have an awareness of the damage fossil fuels have done in smog creation; acid rain that acidified many wilderness lakes and shortened the life of exposed limestone buildings and statues, concrete structures and roads; as well as producing toxic mercury increases in lakes.  The concern about carbon dioxide buildup in the atmosphere causing global warming alarmed many scientists well before Al Gore popularized the problem.  If we were in a global cooling cycle there would not be much to worry about, but that is unlikely to occur without an unexpected drop in solar output or something like a complete melting of Arctic ice providing so much atmospheric moisture that a new cycle of continental glaciation begins.


Quality sounds like an objective assessment could easily be made.  But that is not readily determined until the subjective part has been determined.  If it is a plot of land, do you want to grow orchids or cactuses?  Usually the subjective part is almost implicit in the location and typical use made depending on local environmental conditions.  My early experience focused on freshwater biology, especially bottom fauna of streams.  The principles of assessment of quality are much the same for other habitats as well.

The quality of an environment is most readily determined by observing the living organisms present.  From observations of organisms over their range, along with associated observations of the physical properties correlated with their distributions, we can understand more of the factors responsible for the quality of their environment.

A diversity index is a good way to measure quality without having to be able to identify the organisms.  A sample (standardized if comparison with samples from other locations is desired) is sorted in groups of like organisms, the groups and number in each group is recorded.  The diversity index is calculated using a formula combining the number of groups versus the numbers of individuals in each group.  Low diversity and poor quality of the location starts at no diversity with all in only one group.  High diversity and good quality is indicated by many groups with none vastly outnumbering the other groups.  The results are fairly unaffected by sample size if at least a few dozen groups are included.

The variability of natural locations makes it difficult to characterize the diversity with just a few samples.  An alternative sampling procedure is to use an artificial substrate.  A graduate student doing a research project of analyzing the water upstream and downstream from the discharge of the Kalamazoo sewage treatment plant included artificial substrates as part of his study.  He used small leaf packs anchored and left for a time sufficient for a fairly natural fauna to become established.  The packs could be collected and disassembled so all the aquatic invertebrates could be analyzed.

Many physical parameters typically have a range acceptable for aquatic life.  For example, cooling water or other effluent, may have variable limits based on season, as well as volume and temperature of both effluent and receiving water.  Flow and/or mixing with the receiving water are also considered.  Sewage treatment plant effluents also have limits on residual chlorine disinfectant that can be discharged.


Physical changes in the environment can occur more rapidly than evolutionary changes in organisms.  An organism’s optimal adaptation to the environment will be in a range from minimum tolerated to maximum tolerated.  The optimum may be near the median value or closer to one of the extremes.  Consequently, a change in the environment can reduce survival or eliminate a species; a shift toward the optimum may improve the specie’s survival chances.  Evolutionary changes in a stable environment will usually shift optimum requirements closer to the environmental conditions.  Such stability is not typical so organisms may have a range shift adaptive to geographic shifts in the environmental condition.  A number of organisms have shifted their range northward in North America in recent years.

A study published about the adaptation of Hawaiian fruit flies changing the relative proportion toward an annual cycle of environmental conditions showed a seasonal shift in the abundance of the different variants of the genes involved.  Presumably most organisms have enough heterozygosity (variation in genes) to speed some adaptive changes.

The concentration of salt in cell fluids and blood is close to the concentration in sea water.  It is considered to be evidence of the origin of life occurring in the ocean.  Once animals and plants developed ways of preventing excess water entry or loss and elimination of wastes from their cells and blood they had the potential to migrate to freshwater and terrestrial environment.  Echinoderms are an ancient group that may have converted their excretory organs to other use and thus never were able to invade freshwater or terrestrial environments.

Vertebrates, arthropods, mollusks, annelids, nematodes, and many smaller microscopic groups are commonly represented in most aquatic and terrestrial environments.  Bacteria, algae, and fungi are also widely distributed in all environments.  Vascular plants presumably originated on land and very few have adapted to life in intertidal waters of the ocean.


Not really, but most things are not too much of a worry.  Too much water might increase the danger of flushing out needed electrolytes in the blood.  Too much air from hyperventilation might make you dizzy.  And both could be much worse if they are loaded with pollutants.

 Standards for maximum concentration of an element or chemical compound acceptable in drinking water are set by national, state, or local regulating bodies.  Some things are unacceptable in any amount; radioactive materials, mercury, and polychlorinated hydrocarbons are examples.  But our ability to measure contaminants has increased so much that it often scares people to learn a tiny amount is present.  I would not be too alarmed if anything was present at less than one part per billion; and one part per million is unlikely to be of much concern for most pollutants.  One problem could be that many different related compounds could collectively produce a problem even though each was at a permissible level.  Fortunately, regulators typically set levels at 1/100 or less below the limit at which a small percentage of people are likely to be affected.

Some chemicals such as sodium chloride (table salt) have increased greatly in many of our natural waters.  Limits for drinking water may be due more to possible taste concerns, although one might prefer to keep from adding to their sodium load if they were sensitive to it affecting their blood pressure.  But table use and discharge of salt in sewage could almost be used as a proxy for population numbers before its intense use for salting roads for ice control in northern climates.  There, ground water near heavily salted intersections can have salt levels beyond acceptable drinking water standards.  Salt has leached from underground deposits ever since the early continents rose up with salt beds from once shallow seas.  The return of some salt to the sea is not much of a problem, but other substances are not so innocuous.  Before DDT was widely banned it reached the ocean and turned up in animals that were never near its source; agricultural runoff and urban drains via rivers, and perhaps airborne transport to some extent, may have been the delivery vehicles.

Reduce, reuse, repurpose, repair, recycle may be part of the solution that will help technology minimize the refuse problem.

Joseph Engemann      Kalamazoo, Michigan       October 31, 2016

Thursday, October 20, 2016



A quick Google search confirmed my impression that the dinosaurs became extinct about 65,000,000 years ago at the end of the Cretaceous.  An exception was indicated by referring to the extinction as not including non-avian dinosaurs.  That distinction was made to satisfy scientists who have determined that bird’s ancestral reptilian roots was most likely in a specialized line of dinosaur-like ancestors.  It seems to me that it is unnecessary to continually repeat that connection in discussing non-phylogenetic issues.

Birds are sufficiently different from dinosaurs that they deserve their independency as a group.  Feather’s, no teeth, and homeothermy (maintaining a temperature independent of environmental temperature) may be avian characteristics that had a role in the survival of birds, but that is another topic.


Multiple causes may have operated in making dinosaurs unable to survive the asteroid strike(s) that produced world-wide evidence of the disaster in the geological record found in sediments.  Several other major geological periods ended with similar disruptions, all also associated with the extinction of a large percentage of previously existing species.

In the several billion years of the earth’s existence earth has grown by the impact of space debris of varying sizes as indicated by the assortment of craters on the moon and other planets   Such bombardment was so intense in pre-Cambrian times that animals left a very skimpy fossil record, partially because large fossil forming animals seldom evolved or survived.

The abyss as a refuge during extinction events

The one place that had relatively stable conditions during extinction events was the abyssal region of the oceans.  There, any animals that could survive on the nutrients deposited in sediments had a better chance of survival in some location because most of the earth was covered with deep oceans.  The deep-water pogonophorans were one of the survivors.  The oxygenated region was so extensive and so slow to be replenished by polar surface waters that much of the fauna adapted to the region persisted to the present.  Those abyssal conditions made low metabolic rates and extended life cycles contribute to a very slow, almost absent, evolutionary rate for animals living there. (see 2015/05 listed at end of this post)


Direct hits by the asteroid, its fragments, debris blasted from the impact zone did not even have to kill a single dinosaur.  But the world-wide atmospheric debris may have persisted for a year or more and made it difficult for significant plant growth of the type needed by large herbivores.  Carnivorous dinosaurs like T. rex would miss their normal food after large herbivores starved.  Continents isolated by oceans and partitioned by deserts or mountain rages would have made it difficult for the large dinosaurs to escape the drastic climatic shifts temporarily making their existing range uninhabitable.


Pre-strike population declines or increases may have contributed to the death of many species.  Such declines may have been in the dinosaur species and/or other groups important in their food chains and are not limited to food organisms but could include microscopic disease organisms, parasites, and competitors of various types.  

The complexity of population changes resulting from decline or increase of one species is difficult to predict with certainty.  The decrease in one species may result in survival of more of those they prey upon and fewer of those feeding upon them. The changes can ripple up and down the food, predator, and parasite chains existing in the ecological community.  Add to these changes each of the physical changes produced by each species and the variability of possible community changes becomes astronomical.  If the vast number of buffalos grazing on our prairies had not been replaced by cattle, sheep, and farmers plowing- would much of it reverted to forest or scrubby vegetation providing homes for a different group of animals and plants?  Such changes had far reaching effects including soil erosion, flooding, less retention of water and less rainfall; all changes having additional effects on climate and life.

The cooling accompanying the atmospheric debris which reduced light energy and it warming effect makes a possible sufficient cause for extinction of many dinosaur species by shifting sex ratios of eggs hatching to all of one sex.  It is known that alligators and some other reptiles deposit large numbers of eggs in holes that they dig in the ground.  The holes are then covered over and the deeper the egg in the ground the cooler the temperature it experiences during embryonic development.  Higher temperatures induce one sex, cooler temperatures induce the other sex.  If cooler temperatures make all become the sex normally found in the deeper part of the nest, all will be of one sex.  It is not known if the phenomenon is the cause of alligators being restricted to warmer latitudes.

Cooler temperatures would make animals other than birds and mammals become inactive and unable to respond to egg predation or even being eaten by smaller animals with feather or fur insulation and higher metabolic rates maintaining body temperatures needed for activity.  The immense size of dinosaurs made them less susceptible to short term cold temperatures because it takes days for the largest to cool down, but the asteroid caused global cooling would persist so long it might have been sufficient to cause their demise, even those many other causes may have speeded the process of extinction.

Joseph Engemann     Kalamazoo, Michigan     October 20, 2016 

Monday, October 17, 2016


During the "Cold War", and at other times, Russia was among the nations making accusations about their enemies.  Many times it seemed to me that it turned out that they were the very ones doing the evil deed of their accusations of others.

[election campaign commments deleted 11/13/16]

Joe Engemann      Kalamazoo, Michigan     October 17, 2016

Friday, October 14, 2016



Dear Jessica,

I was like the guy across the aisle that did nothing to help you.  So I may know why the passenger that may have been watching a molester molest you also did nothing to help you.

In 1952 I was a U.S. army soldier on a train somewhere between Paris and Munich with just three in the car.  I was a few seats away from a young (German?) girl who was probably in her late teens.  Another soldier entered as we left the station and sat briefly a short distance from us before getting up and seating himself next to the girl.

It didn’t take him much time to begin trying to engage the girl in conversation which terminated when it was obvious he did not speak German and she did not speak English.  But that didn’t deter him from putting his arm around the girl, much to what seemed to me to be her discomfort.  Very soon he had one of his hands on her, still clothed, breast.

During the process I was becoming more alarmed and considering what to do.  I was considerably bigger than the offensive soldier.  It seemed possible that an altercation might delay my return to my base in Munich beyond the return time of my leave termination.  I didn’t have much confidence in my ability to explain things to the civil authorities.  And then the couple became more congenial and departed together at the next stop.

If her discomfort would have escalated or she would have indicated the need for help I would have tried to help.  I still feel I should have done something because I don’t know the outcome for the young girl.  I don’t think I have told my wife about this episode in my life.

I don’t think I had any fear that the girl would attack me if I tried to defend her.  Such a response in not uncommon when police try to stop a couple’s domestic disturbance.

The guy across the aisle may have been lulled into thinking you and your molester were a pair due to your conversing and eating next to each other.  None of that is an excuse for the slimy behavior of your attacker.  He probably honed his molesting technique by many previous episodes to minimize negative reactions to his behavior.  It seems to have become such a part of his character that he no longer recognizes nor remembers his shortcomings and may not even realize he is lying about them.  His frequent legal and other threats show he has not learned much to advance beyond petulant childlike behavior.

 Thank you for coming forward.  It is good to know that the attack did not deter you from becoming a delightful senior citizen as attested by your friends and what I have seen on CNN.

[some editing and deletions 11/13/16]

Joe Engemann      Kalamazoo, Michigan    October 14, 2016

Thursday, October 6, 2016



Evolution shows alpha males arose in numerous evolutionary lineages.  They result from the selection favoring their greater reproductive success.  That can occur by dominating lesser males and driving them away from protective value or the group that includes the fertile females.  As a result they monopolize the female insemination job and pass on the genes for that behavior.  The larger, stronger, meaner males may also result from the females passing on genes that favor selection of larger males by their reproductive success in groups favored by such behavior.

Fitness of males does not need the large size if some other selective factors are operating.  Many birds have gorgeous males that put on a great display of their plumage in dances or behavior that may also speak of their health and energy, factors also associated with success,  The females that select such healthy mates also contribute to selection of such pairings if they have the expected greater reproductive success.

Primate lineages with big, strong, mean alpha males retained those features in the case of gorillas and chimpanzees to some extent.  But the value of an alpha male diminished or even may have been an unfavorable selective factor in the primate line leading to humans.  The social family and tribe groupings had selective value continuing to the present for humans.

Humans work together and accomplish many things contributing to our success.  Traces of alpha male characteristics remain and even had value before modern society evolved.  The selective value of the nuclear family that provided a small team to rear the slowly maturing young has not completely disappeared.  But God had waited long enough and finally came to us with the message to love one another as we love ourselves, a duty that is only secondary to loving God.

[references to the president-elect deleted 11/13/16]

Joe Engemann     Kalamazoo, Michigan     October 6, 2016