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