Friday, December 30, 2016

Honeybee: Poems


Naomi Shihab Nye's 2008 book, Honeybee: Poems, is a delightful book of poems and prose with observations that are very thought provoking in numerous ways.  My daughter had not read the book but had heard the author at some poet's meeting where the author had read the fourth selection, "Museum".

Before I was aware of that I had commented to my spouse that it was a selection I wanted her to read even if she did not want to read the book.  I had read her a couple of snippets from other entries and by the time I was one-third of the way through the book felt it was a must read for everyone who values peace, kindness, the environment, and all people.

As one who did not take the time in the 50's, 60's and 70's to tap the content of popular culture of those days it was refreshing to get a taste of it that I suspect others got in the music of the time.  Pages 77 to 109 have a few entries that might distress people who do not want their status quo disrupted.  So if you had some distress getting to page 77, skip to page 110.  at the very least, read the last selection, "Gate A-4".  I hope you read many more and find your favorites.

Joe Engemann    Kalamazoo, December 30, 2016.

Honeybee: Poems by Naomi Shihab Nye is a 164 page Greenwillows Book imprint of Harper Collins Publishers.   www,   If you read the book you will find out more about her and what stimulated many of the views I hope you will also appreciate.

Thursday, December 15, 2016


Formation of Organic Molecules, the Haldane-Oparin Hypothesis

The early chemical steps toward life have a good theoretical basis.  The basis is found in a 1920’s hypothesis credited to a Russian biochemist, Alexander Oparin, and an English biologist, J. B. S. Haldane.  Each hypothesized the first formed atmosphere lacked oxygen, but contained ammonia, and had reducing properties.  The chemicals of the atmosphere interacted in the presence of ultra-violet light, lightening, and volcanic heat to produce the chemical precursors of living systems.  Biologists think the precursors accumulated in the water and somehow assembled into primitive living systems.  Such steps were necessary because free oxygen is produced by photosynthesis and would not have existed in abundance prior to photosynthetic organisms.

The ammonia was formed as it can be today from the effect of lightening upon atmospheric nitrogen and water vapor.  Carbon dioxide was abundant in the early atmosphere.

An experiment in 1953 by Stanley Miller and Harold Urey in Chicago . . . . . .used sparks in the atmospheric portions of the system to simulate lightening.  They cooled a portion to condense water along with products in solution that were present or produced.  Analysis of the condensate showed some amino acids and other organic compounds, most of which are components of living systems.

Concentration of Organic Molecules

The most important mechanism may have been concentration by evaporation of water.  Low tide could have made it a daily event in intertidal areas.  But higher splash zones may have had longer periods of isolating pockets of water for greater concentration.

A second mechanism is by coacervate production.  The coacervates are small globules of organic material that accumulate other organic molecules because their solubility in each other is greater than their solubility in water.  This . . . . . .could have been the route of biological membrane formation.  Membranes . . . form naturally in systems where an abundance of the proper lipid molecules are present.  The water insoluble ends are semi-dissolved in each other and repel the water soluble ends so a double layered membrane forms automatically.  The third mechanism, adherence to particulate items may have been especially prominent in pockets of water along the shore.  It might be thought of as the “bathtub ring” origin of life.  It is perhaps the least certain of mechanisms, but seems a possible explanation for aiding the origin of some of the biochemical processes where minerals are important components.  
[The preceding is adapted from pp. 74 and 75 of my 2009 Evolution Insights unpublished manuscript.]

Alternative Views of Organic Molecule Formation

An alternative view of the origin of life was proposed by a marine biologist, Corliss, who, noting the abundance of life at deep sea vent locations where the animals surround volcanic heat and emissions produced chimneys, suggested such sites were where it all started.  An earlier experimental observation by a scientist at a newly formed island near Iceland showed that lava and seawater interact to produce a few amino acids and small organic molecules.  In the early history of the earth lava/seawater interactions were presumably more widespread and included many more shallow water locations.   Such locations undoubtedly contributed to the organic content of the original oceans but are unlikely to have been the location where animals originated for two reasons.  One, they come and go with change in lava production and are limited in geographic extent to mostly where crustal plates meet.  Two, the fossil record indicates older forms of life seem to have originated in shallow coastal areas and progressively over time show representatives in deeper waters.

Few accept biblical accounts of creation of life details.  Certainly, God could have created the world and its inhabitants, fossils and all, in a short time, but doing it in the billions of years and with the details supporting the amazing story of evolution seems like an even grander way and leaves people with the kind option of not demanding immediate belief in an infinite deity that is all loving, kind, and merciful.

Evolutionary Consequences of the Haldane/Oparin Hypothesis

1.       The first compounds formed, including such amino acids as glycine and adenine, became important building blocks for living systems.  Adenosine triphosphate, the energy currency of the cell, and the unique structure of DNA with adenine as the basis for one of its four nucleotides of the genetic code, were important consequences.

2.       Functional values of early steps were retained as basic, but slightly modified, characteristics seen in descendant organisms.  The gradual changes leave helpful clues for tracing the evolutionary history of animals as well as plants.

3.       Photosynthesis, upon which we are so dependent today, makes shallow seas and coastal regions the most likely place of life's origin.

4.       DNA’s early origin before the oxygen laden atmosphere developed meant the development of the nuclear membrane probably developed after photosynthetic bacteria.  The nuclear membrane enables DNA to operate in the part of the cell where it experiences the cell's lowest oxygen content area most like it experienced in its early origin.

5.       Billions of stars have planets where now or in the past similar conditions led to production of the same basic building blocks.  Such beyond earth production makes it quite possible that fragments of extraterrestrial bodies containing such organic compounds may have impacted earth without proving life was present on the source planet.  Planets in other galaxies, as well as in the Milky Way, have undoubtedly had similar periods with similar conditions to earth with somewhat similar evolutionary histories of life.

Joseph G. Engemann, Emeritus Professor of Biology, Western Michigan University, Kalamazoo        December 15, 2016

Friday, December 9, 2016


Evolution and Pharmaceuticals

During the course of the evolution of life on earth, species were faced with many challenges.  Over time, a mold tailored a chemical to a point where it prevented bacteria from interfering with its growth.  Alexander Fleming noted that inhibition of bacterial colonies on a petri dish around a fungus that contaminated the culture.  The happy accident and his observation of the effect of penicillin led to many searches for other fungi that might be producing other antibiotics. 

We have a more versatile bacteriafighting method in our immune system.  It can even fight against toxins, given the right circumstances.  We can induce other mammals to produce antivenoms in their serum to combat potentially lethal snakebites when injected after a bite.  Are there other marvels of nature waiting to be discovered by our pharmaceutical industry?

Groups, especially sponges, that are attached to the sea sediments or rocks, have an evolutionary history of over half a billion years.  Their major defense against microorganisms such as bacteria may include physical barriers, such as mucus secretion, but there has been a wide assortment of toxic materials, some of which provide protection against predators and others probably against microorganisms.  It seems such knowledge could provide a wealth of useful products.  I think the major thrust has been to look for anticancer activity in such products.


Control or lack thereof

The hereditary changes determining the speed and direction of evolution are not subject to control nor are they controlled by some foreseen outcome of the process of natural selection.  Many possible random events producing changes in the DNA produce a range of possible variations in individuals.  The survival value may be valuable in one habitat, but detrimental in another.  When the habitats occur in different parts of the range, the one species may become two or more species as accumulations of differences become great enough that the extremes can no longer interbreed successfully with each other.

 The survival or death of a variant may be due to chance meeting with a predator.  A falling rock may select traits by eliminating those of individuals too slow to see and escape, but its selective action would be random for traits not involving sensing its approach and facilitating rapid evasion.

In the billion years animals have existed, and the millions of species present now and during many of those billion years, there have been uncountable selective events resulting in compounds useful for survival, and far greater numbers of events that were useless or harmful.  But the harmful ones reduce the chances of their bearers surviving.  The result - many millions of possible useful substances still to be discovered are out there in nature.

Speed of evolutionary change

Early in the evolutionary lineage of groups of related organisms change was probably quite rapid as compared to groups that have not radiated into all available habitats.  Well adapted species may change very little.  This is evident in the fossil record.  One of the more astounding ones is Lingula, a brachiopod living today, whose shell is much the same, except for size, as a Pre-Cambrian fossil brachiopod shell.

The speed of evolution of things affecting survival can be quite rapid when there are great differences in survival value involved.  Most fish are well streamlined, so little drag enables easy progress through the water.  Birds are also streamlined, but their streamlining is of most value at high air speeds.  Natural selection maintains the streamlining for both fish and birds.

Direction of evolutionary change

Different species of the same group may be evolving in different directions.  For example, most mammalian groups, such as rodents, carnivores, and primates have radiated into different sizes.  Those particular examples have mostly started from relatively small ancestors.  But several vertebrate groups show the largest species are only known from fossils.  Direction is not typically linear.  The long ancestral line from early life to us and most higher animals went through a regression from annelids to the pogonophorans before advancing to the groups leading to the vertebrates. 

The genetic basis of the above

Most inherited characteristics of animals are multifactorial, that is multiple locations on the DNA may affect the expression of the characteristic.  Some may have one locus that may have an all or none effect on the expression of a characteristic.  Other characteristics may have more complicated inheritance.  All aspects of a species are subject to evolution; besides physical and physiological features, life style, life cycle, and other features evolve, sometimes independently, but often in conjunction with other features.  Improvement in one aspect of our physiology can have far reaching effects in many systems.  Conversely, diseases are often characterized by many symptoms.

 Sickle cell anemia is an example where the substitution for one particular amino acid in a long hemoglobin chain modifies the structure of the hemoglobin molecule.  Heterozygous individuals have less expression of the gene into the fibrous form, but their red cells have enough to provide protection against growth of malaria parasites.  So natural selection maintains the disease in areas where malaria kills many without the gene, and the disease kills many homozygous for the gene (i.e., inheriting it from both parents).  But in areas where malaria is not present, the frequency of the gene is expected to diminish due to higher mortality of those with the disease.

Environmental control of gene expression

One of the examples of environmental control are the two color-phases of animals in arctic and subarctic locations.  In summer, several species of mammals and birds have fur or feathers of darker colors than the white shown in the winter.  It is protective coloration for prey species with the seasonal change, as well as enabling predators to have greater success in getting closer to prey before they are alarmed.  Apparently, the colder temperatures prevent expression of the pigmentation genes.
I suspect my white hair is a result of lower activity resulting in skin temperature needed to make the melanin for my long-gone youthful dark hair; the benefit is many young people holding the door for me.


Quasi-genetic control of gene expression

The existence of introns and exons suggest a possible mechanism of graded responses of genes since so much of the DNA is not serving as a template for RNA producing the physiological and/or structural biochemical actions of the genome.  Think how the length of the “inactive” space between genes may moderate or accelerate reaction to an adjacent promoter or inhibitor gene.

The enzymes acting are usually proteins with an active site held in appropriate form by seemingly inactive parts of the molecule.  The inactive parts have parts that can undergo substitutions of minor portions that may not have much effect on action.  Hormones may have similar flexibility. 

Drug manufacturers take advantage of such flexibility to produce new versions of medications that can then be patented to replace the original that is going off patent.  Some molecules receiving such modification may have changed effectiveness in unpredictable fashion with no change, bad changes, or good changes.  Toxicity, solubility, and other factors make it nearly as big a screening problem with pre-clinical and clinical testing before marketing.  But the economics of keeping it on patent and high priced is important to them and makes it profitable.

Designer drugs

Physical chemistry and computers have become capable of visualizing three dimensional structures of molecules.  Knowing the structure of some significant portion of a bio-molecule makes it simpler to design chemical molecules that will bind to the site and bring desired structure to the rest of the molecule.  There seems to be no end to the possible applications.  I doubt that the computer will be able to do all the thinking and evaluation that a competent research team can bring to complement the task.


A great drug company, The Upjohn Corporation, was started by a local physician who developed the friable pill.  They were an excellent employer and blessing to the community.  Several mergers later, they are now Pfizer.  Along the way research teams were disbanded in downsizing the merged research effort.  The emphasis is now on buying up small innovative companies to stock their new-drug pipeline.  I don’t know of any successes of the computer-driven drug designing, although I am sure it has yielded some benefits at the cost of losing possible greater benefits from the old research teams.

Now and then there are hints of and actual spin-offs of businesses.  The drug company business types and corporate boards can now reward themselves outrageously like many other businesses do.  Shareholders, employees, and communities suffer with the shenanigans.  Short term rewards imperil future benefits.  The vast majority of executives are honorable and hard-working, but one persuasive senior executive can do a lot of damage in their grasp for material success. Make a big deal of the mergers or downsizings achieved and get a big bonus in dollars or shares at everyone else’s expense.  Pfizer is still a good company.

Joseph G. Engemann    Emeritus Professor of Biology, Western Michigan University, Kalamazoo
December 9, 2016

Monday, November 28, 2016



Elizabeth Johnson's book, Ask the Beasts was mentioned at the end of the previous post.  On pages 7 to 9 she discusses science (evolutionary theory) and religion (theology) interactions.  She notes four ways of interacting described by Ian Barbour in his 1990 Gifford Lectures.

The first type of interaction was conflict.  As evidenced by fundamentalists insisting literal interpretation of Genesis proves evolutionary theory is simply wrong, and atheists countering with the argument of science that evolutionary theory is backed by the creation of life and its variations by the chance processes of evolution and natural selection which proves God does not exist.  Neither side admits to the flaws in their arguments so the creation/evolution/debate keeps resurfacing.

The second type of interaction, independence, is more a lack of interaction due to lack of overlap in their areas of operation.  This may be a practical solution and not a admission or right or wrong in the position of those outside their main area of interest.

The third type, dialogue, attempts to resolve the differences in positions by gaining new insights into religious teachings and their meanings.

The fourth type, integration, carries dialogue a little farther and might achieve recognition of God as the source of the laws governing the physical world,

Johnson proposes practical cooperation as "a fifth model of interaction that I would add to Barbour's chart, . . . . . .for the preservation of the natural world."  There certainly are both religious and scientific grounds for cooperating on common ethical standards for preserving the natural world.


Conflict is inevitable when you take a strong stand in the creation/evolution debate that frequently arises when advocates of special creation contend with mainstream science over the teaching of evolution as the origin of species (especially humans), by means of natural selection, in science classes of public schools.

The flawed arguments of those most vocal adherents of special creation are very convincing to those whose training in science is is limited.  Many may become internally conflicted or experience cognitive dissonance trying to resolve the question.  Both arguments seem persuasive.  So who is right.


When I taught about evolution I tried to present the scientific facts about the operation of evolution and the evidence that exists.  Mindful of the distress experienced by those indoctrinated in literal interpretation of Genesis, I pointed out that an all-powerful, infinite creator, could create the fossils and species of living organisms in seven days or any desired timescale,  I did not think that belief was necessary,  I don't remember if I told them I believed God created the world and all the natural processes science has discovered.  I probably told them that others believe it started with the "Big Bang."  It would seem that scientists would recognize God as the cause for that moment of creation.

I don't think anyone has had a valid revelation about all the details of how God created and sustains the world.  The operation of natural laws created by God are sufficient to explain the evolution of the world by means of natural selection.  But natural selection has random events that make the history of the species on the earth very complicated.  Sometimes we see selection leading to gigantism, sometimes to great size reduction.  Side branches of the tree of life lead to many groups showing great diversity, often radiating into scavengers, herbivores, predators, and parasites.  Certainly, God is the creator of all those things, whether by one astounding act of creation, or with continual input into the process.  My saying so does not make it so, although I would opt for the one astounding act of creation.  I know God sometimes accepts special requests and clearly did numerous miraculous things from the time of Abraham to the present, with the special highlight of events over thirty some years beginning about 2016 years ago.

Many have made their choice, so conflict will continue for them.

Joseph G. Engemann     Kalamazoo, Michigan    November 28, 2016

Wednesday, November 23, 2016



In a recent book [Axe, Douglas.  2016.  UndeniableHow Biology Confirms Our Intuition That Life Is Designed.  Harper One, HarperCollins, NY, NY. 298 pp.], Axe uses the flawed logic of the “Intelligent Design – Special Creation” community in an impressive attempt to support childhood intuition of cause and purpose as an indication of the truth of the special creation of each species.

Once special creation is assumed for species creation, on the basis of childhood intuition, he postulates that all things have a cause and are made according to plans that the creator uses to produce each species.  He “proves” this by showing the statistical impossibility of DNA sequences specifying one characteristic ever being produced by a chance result by his view of natural selection.  Unfortunately for him, natural selection does not operate in the direction he assumes.  It is not really selection of the new variety, it may just be the failure of the old variety surviving or not expanding into new territory to which the new one may be better adapted.

For a concrete example consider human pigmentation.  Presumably, as we evolved in Africa we survived there better by having high levels of melanin pigmentation in our skin.  That provided several possible benefits including protection from overproduction of vitamin D in the skin and damage from high levels of U-V light in the tropics; those living in tropical forests had coloration making it difficult for predators to find them, whereas in savanna and desert the dark color absorbed more heat sooner in the morning to improve their morning activity start.  Conversely, those migrating to colder climates benefited by, partial loss of pigmentation that allowed enough vitamin D to be produced, and less visibility to predators where snowy conditions occurred.

More than one gene is involved in melanin production and each requires several biochemical steps.  The loss of any portion of the proper sequence of biochemical events can result in reduced melanin production, and if all genes have interruption of the process, the person will lack melanin pigmentation.  A similar process operates in most species, so changes (mutations) in the hereditary material have many ways to produce albinos.

The speed of such a selective process operating is shown by the fact that cave dwelling isopods in the central United States are most like the surface dwelling isopods nearby but lack melanin and eyes, among other cave-dwelling adaptations.  Mutation rates are such that studies seem to show that deleterious mutations seem to occur at least ten times more frequently than beneficial ones (with exception of where the loss is beneficial as noted for albinism).

So, mutations needed for evolution are random events producing inheritable variations in the DNA of a species.  The change does not get selected at the gene level, the selection is at the organismal level as a result of the survival value in the organism’s environment.  At the gene level, it is possible that loss of a feature may be just as important in evolutionary result as the gain of a new feature.  The potential for graded responses due to interactions within the body may complicate the process but evolution is neither a conscious process nor a struggle toward a particular goal.  That does not preclude the process from being directed by the Creator from before the creation of the universe.  That cannot be determined by the tools of science, nor by our philosophical or theological musings.


A slightly older book than Axe’s book is one by Elizabeth A. Johnson [Johnson, Elizabeth A.  2014.  Ask the Beasts: Darwin and the God of Love. Bloomsbury, London (2015 paperback) 323 pp. + XVIII.].  The book has outstanding coverage of evolution/God/science/theology/ecology.  The eighth paragraph (page 240) of chapter 9, Enter the Humans, has great coverage of human advances.  On pages 5 and 6 environmentalists will appreciate her statement of the horrible state of the earth.  And her pages 7 and 8 contain a concise presentation of the fallacy of the creation (intelligent design) versus science (evolution) debate.  I have not completed reading the book, but my sampling makes me give it an endorsement of outstanding.

Joseph G. Engemann    Kalamazoo, Michigan      November 23, 2016


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

Monday, September 26, 2016



Meeting your maker is an ominous phrase that is used to imply a first introduction upon passage into eternity which we hope or believe will be our eventual fate.  But we don't have to wait that long.  Our first introduction in not likely to be as dramatic as that the apostle Paul experienced when he was knocked to the ground on the way to Damascus (Acts 9:3-5),

Most of us are likely to experience our first awareness of meeting God the way the Old Testament writer did in the gentle breeze following the dramatic natural phenomena he observed.  Others recognized the physical grandeur of the world and the living inhabitants as his works.  Many still feel a sense of awe in quiet moments observing the same things,


You don't have to wait for a desperate death-bed plea to meet God.  But you have to recognize that God is unlikely to use a burning bush or some other dramatic sign of his presence.  You can avoid meeting God personally by convincing yourself the circumstance was a chance happening or a psychological aberration.  So what are the circumstances likely to give you your introduction.

I suspect an old-fashioned tent revival meeting with a dynamic preacher could be a start.  But my experience makes me think a more gradual spiritual  growth may be more sustainable.  I think there may be some ground rules for making spiritual progress.

Ask for God's help in your journey.
Don't blame God for your problems,
Ask for God's help in dealing with your problems,
Thank God for the good things in your life.
Do what you can do for yourself.
Do what you can do for others.

I think I have had multiple reintroductions to God acting in my life.  One that is available to most of us is to find God in scripture.  I never completed reading the Old Testament after several attempts.  The historical books were a bit much for me,  But Psalms, Proverbs, and some of the shorter books were more manageable.

It is worth trying what Charismatics call "cracking the book".  Open the Bible to some random page and read the first thing that catches your attention.  It was amazing to me how frequently a passage came up that seemed to address an area of personal concern.  I seldom do that anymore, it has been supplanted by daily readings of Old and New Testament texts assigned according to a liturgical calendar.  A booklet with accompanying reflections is often inspirational.


"My Evolution Blog" was my first post.  Then (May 9, 2013) I was perhaps too excited to put my name and the date on the blog.  Perhaps I was a little skittish about security concerns and retaining my anonymity.  I was 84 at the time and had already lived five years beyond what I had expected after diagnosis of a blood disorder.  I thought the Lord had given me a little more time to complete the manuscript upon which this blog was based.

Well this blog, which was to substitute for publication of the manuscript, was finally started after a remarkable stop of another health problem.  Now, over three years later, I am well recovered from hernia surgery that had been put off for many years.  It is relatively minor surgery, but my lack of enough blood platelets means surgery is more risky.  A platelet transfusion just before the operation minimized the blood loss although my blood hemoglobin dropped about 20%.  I look at the numbers on the printout  of my blood count etc. and realize why physicians are concerned,  But I feel fine in an age adjusted way and am content that I have blogged about the main things I thought I had to say about evolution and God.  So now I will probably continue with things I find of interest and think some of you may share my thoughts.

Earlier in the day I thought I might blog about a few "zingers" I might provide the two main candidates for their first debate tonight.  But I thought I better do the above, three earlier versions of it had already slipped my mind.  I thought they were great, but I went to bed and did not remember them clearly the next day each time.  So now I will return to other topics for my next blog post.

Joseph Engemann      Kalamazoo, Michigan    September 26, 2016

Tuesday, September 13, 2016



 Wonderful people can come upon hard times physically, emotionally, and through various disabilities associated with accidents. aging, diseases, injury, abuse, poor choices, and various personal and natural disasters.  Some are chronic conditions that may have solutions or relief in ways not understood by the afflicted.  Family members may come to need help with the situation as much as the one perceived to have the disability.  I decided to share my views through this blog when I became aware of someone close to me who was trying to help a couple with a problem.  I wanted to talk to the couple to share some of the things in this series of posts.  But I was not in a position to do so, and I thought there were many more people needing the same coaching, so these posts might meet the needs of more without the abrasive aspects of my personality interfering.

When social agencies are not sufficient, and even when they are, prayer is worth considering.  The five following posts (posted over five preceding dates) are somewhat geared for the more serious personal problems, but God is there for us for much lesser things, often without our asking.  They may be helpful early in the process before the individual(s) become the subject of a family intervention, or if there is no one to intervene.

The anecdote about the driver almost late for an important appointment and circling the rows of the filled parking lot thinking “God if you find me a parking spot I’ll make a big donation to charity”, then as the corner is turned revealing an open space continues thinking “never mind, I found one myself,” may help us see how we operate when needs are satisfied.  Solutions arrived at through requests for divine help can easily become past history, especially when a natural event can be seen as the cause.  Before modern medical help for childhood asthma was available I was not able to even think of praying when I was gasping for breath during severe episodes.  But those times passed relatively quickly though they seemed like an eternity.  I don’t have all the answers, so you should be able to surpass me in your understanding.  Having something to think about is a beginning.

The five following posts listed were posted in reverse order so they would be archived in proper order for those who proceed down the sequence from this one.

Post 2 – Eligibility may help you realize everyone is created by the same God and is loved as a child of God.

Post 3 – Expectations may prepare you for answers to your prayer that aren’t exactly according to your specifications.

Post 4 – Who to ask may help if you are intimidated by approaching God directly.

Post 5 – How to ask may give you some comfort in the form of your plea.

Post 6 – Saying thank you has benefits.

Joe Engemann      Kalamazoo, Michigan     September 14, 2016



Your eligibility for receiving a miraculous cure or other aid came with your birth as a child of God.  Do you think the only God created you with an evolutionary process of near infinite complexity and duration and then would give up on you?  Not a chance.  is an early post that may give you a reason to think God loves you.  If you read the Bible you can see how even people with serious failings were and are loved by God; but that is not an endorsement for deliberately failing.  Jesus makes statements showing that God desires salvation for all of us.  Luke 4:38-44 is a gospel reading that tells of Jesus curing many with no indication of his using an interrogation process or evaluating them.  Moses and David play significant roles in the history of God’s people and each was involved in the killing of another person.

To determine your eligibility for divine help, use the following check list and check items that describe actions you did without being forced to do so,

Have you ever? -

___ smiled at someone
___ helped someone without being asked
___ complimented someone
___ put a penny in a donation receptacle
___ donated a million dollars to charity
___ helped in a soup kitchen
___ put a dollar or a dime in the Salvation Army bell-ringers pot
___ said a prayer for someone else
___ said thank you
___ voted for the best candidate

Count the number of checks.  If 0, keep trying.  If 1, you are eligible.  If 2 to 10, you are still eligible.

Remorse for past moral failings is often expressed by prisoners who seem to accept their confinement.  Unfortunately, the legal system is not geared up to return them to a free life, execution or confinement is still continued, but they are often more content (I have no statistics to support this statement, just a lifetime of reading news accounts and magazine articles of such instances).

People in danger of death during wartime and peacetime personal disasters that usually do result in death have appealed to God and received remarkable and miraculous rescues.  I used to keep such things in a file, but most were a bit long to include here, even if I could find them.

I have been the recipient of a few things that I put in the miraculous category because they were so swift in timing and duration.  Because some involved personal failings and/or are of embarrassing content I will not relate them.  If you have such things, talk to Jesus about them, he already knows more about it than we do.  Then don’t dwell on the past, accept the present, and just revel in the future.

Joe Engemann    Kalamazoo, Michigan     September 13. 2016