GOD, EVOLUTION, AND THE POPE

Pope Francis

According to an October 30, 2014 news release on the Religion page of huffingtonpost.com the pope talked at a meeting recently to some scientists about evolution being an acceptable way of viewing the method by which God created humans.  This apparently has been an acceptable view since it was indicated by Pope Pius XII during the 1950's.  It has not been very popular with many in the hierarchy of the Roman Catholic Church, most notably with one of the leading cardinals, who, several years ago, expressed his view that evolution did not seem capable of leading to the extreme complexity seen in humans.  So the view of Pope Francis is welcome, as you can infer from many of my earlier posts.

My 2010 Evolution Insights book manuscript has  Appendix 4, Chance and The Origin of Man, discussing some of  the above on seven pages beginning as follows

"This appendix has been shaped largely by consideration of arguments presented by Christoph Cardinal Schonborn, author of the 2007 book entitled Chance or Purpose.  His book was written to clarify his position expressed in a July 7, 2005 New York Times article titled "Finding Design in Nature".  A final section will quote from an excellent new article showing that others in the religious establishment do not share the view of Chance or Purpose."

I was alerted to the Huffington Post item by another daughter who thought I would find it interesting.

The appendix noted above has a section on teleology, the philosophical belief in all things being created for and directed toward an end, and notes that it "is fine for religion, debatable for philosophy, but counter-productive for science."  Seven other sections included The Faith and Morals Side, Overextending philosophy/theology, Our unique brain, why we are all so smart, Obstacles to agreement, The role of chance in evolution, Intermediate causes and the final cause, and A refreshing voice.  I may leave those without comment unless interest in them is expressed.

Joseph G. Engemann      October 31, 2014

WMU MAGAZINE BEE ARTICLE

BEES AND ECOLOGY

The Fall 2014 issue of the Western Michigan University Magazine is available online if you log in to wmich.edu/magazine or click the following - Western Michigan University Magazine and click on the issue.  If you use the Google Chrome browser you can easily scroll through to a few pages detailing the work of a group of WMU student's efforts at bee-keeping.

The article tells of the importance of bees in pollinating many of our food crops, and some other things of interest.  There are many things of interest about bees that I could add but they are mostly familiar to those with a biology background.  Communication among bees, colony structure and individual roles, foraging behavior, anatomical specializations can be found in many biology texts.

The issue has several other articles of general interest, especially one about one of the lost boys of Africa, and one about story-telling in Africa.  Of current interest, an interview with a WMU virologist, about the reason North America is not likely to have an Ebola epidemic similar to the one in parts of Africa, coincided with today's news reports of those dealing with recent cases here.

ENVIRONMENT

American Earth, Environmental Writing Since Thoreau is a 2008 anthology edited by Bill McKibben.
The 1048 pages are copyright by Literary Classics of the United States, New York, NY and distributed by Penguin Group (USA) Inc.  A daughter gave it to me yesterday and it has a lot I hope to read and some selections from books I have read such as two landmark books, Silent Spring, by Rachael Carson, and the earlier book by Aldo Leopold, A Sand County Almanac.

My interest has probably been more in the environmental area than the evolution area.  My posts have emphasized evolution because there is more clarification needed there.  The environmentalists are mostly on the right track so I don't feel an obligation to write about it as much.

Joseph G. Engemann   Kalamazoo, Michigan  October 23, 2014

MOLECULAR BIOLOGY AND EVOLUTION

Molecular clues to evolutionary relationships

Before molecular phylogeny, with varied nucleic acid studies became an important part contributing to our understanding of the tree of life, there were many precursor applications guiding our attempt to classify plants and animals.

Molecular evidence guiding our view of evolution, was compatible from the earliest days, with our classification schemes based on the assumption that each species was discrete from others and separately created.  Today, we know that the origin of species from prior species was a gradual process dependent on the accumulation of numerous changes preceding the advent of reproductive isolation of new species from their ancestral species.  The separation of new from old is typically enhanced by other isolating mechanisms of location, time, and changed aspects of biology.

Chlorophyll, or its green color, was an early clue separating plants and animals that must have been known before written records developed.  As molecular biology developed, we found that there are different variants of chlorophyll and photosynthetic pathways.  Green algae and blue-green algae are easily distinguished from one another by the color of their chlorophylls; they also have many other significant differences not involving color or chlorophyll.  There are efficiency differences, between the C-3 or C-4 pathway, and vascular plants abilities to convert solar energy into glucose which can be stored as sugars and starches.  

Cellulose, a polymer of glucose, is a structural material of plant cell walls that is lacking in animals. 

Insect and other arthropod exoskeletons contain chitin.  Chitin is limited to animals known as protostomes, and is not found in the other main branch of animals leading to vertebrates.  It is a polymer that can be broken down into n-acetyl glucosamine by the digestive processes of a few animals.  Surprisingly, cellulose and chitin digesting enzymes are uncommon in most higher animals, so those using them as a food source usually need the aid of microorganisms.

Plants and animals have many basic molecular features in common.  Nucleic acids, with their many functions for inheritance and production of protein, are one of the first shared features common to all cellular organisms.  Adenine and glucose are two of the substances produced when simulations, of the pre-biotic earth atmosphere and physical factors, are conducted in the laboratory.  Adenine is especially notable for its role in formation of one of the four nucleotides making up the genetic code.  It also is essential in adenosine triphosphate, whose high energy phosphates power many biochemical reactions in living organisms as they use the stored energy originally produced as glucose in plants. 

Hidden Origins of Similar Compounds?

Most biochemical molecules we often think of belonging to recent groups may have had origins much earlier than current evidence shows.  The presumption is that two different groups having a unique compound must either represent descent from a common ancestor or they must be a case of convergent evolution.  But compounds active in minute amounts, such as hormones, may have been present in common ancestors in such low levels they have not been detected.

One possible bit of evidence might be the presence of ecdysone, a hormone important in controlling molting of insects, has also been found in bracken ferns.  If it were present at extremely low levels, in ancestral species reaching back to a common ancestor among one-celled organisms and had little use, it might not be detected until it was produced in sufficient amounts as part of a new process to benefit insect molting.  The near ancestors of bracken ferns that developed increased levels of ecdysone sufficient to disrupt fern-eating insect adults and/or larvae would eventually survive better and replace those being killed by insect activity.

The long periods involved in evolution of different forms of similar compounds is likely to allow the demise of intermediate stages of the evolution once a perfected solution is reached.  Until the activity of a substance is useful in larger amounts there is a selective advantage of not making larger or detectable quantities.  So a substance produced in the cell and doing an activity within the cell by inducing gene action within the cell is not needed in the high levels the amounts hormones transported by the blood require.  My attempt to discover "protozoan hormones" as noted in an earlier post was based on this line of reasoning.

The Genetic Code Evolution and Phylogeny

Non-coding regions of DNA are most likely to be more alike in rates of evolution than are the coding regions.  Unless a region codes for a more important function than merely connecting the coding regions of a chromosome there will be little impact on natural selection rates of retention or elimination.  Spacing effects are an example of how non-coding regions could be involved in changing biological function rates.

The example of cytochrome c, a compound required by all higher animals and one of the first successes of molecular phylogeny relating diverse phyla, should be revisited.  The use of the polymerase chain reaction (PCR) for studying nucleotide sequences might be applicable to the regions of DNA coding the cytochrome.  The data could then be used for groups where adequate amounts for comparing cystochromes were not available at the time of the original study*.

*Fitch, Walter M., and Emanuel Margoliash.  1967.  Construction of phylogenetic trees.  Science, 155:279-284.  [20 Jan 1967]

Joseph G. Engemann    Emeritus Professor of Biology  WMU, Kalamazoo    October 17, 2014

HABIT

HABIT, CREATIVITY, EVOLUTION, AND GOD

Habits may seem like worthless attributes, but they are important in the way we function.  Sometimes they are beneficial in accomplishing routine tasks; at other times they can lead us astray at critical decision-making times.  Today, one provoked thoughts, of many aspects of their influences on us, while I was showering.

My habit upon arising soon moves into shaving, brushing my teeth, then showering.  Often, as today, I was still a little foggy from just awakening.  Reaching for the toothpaste, I reached for the tube that was nearly depleted of toothpaste.  Fortunately, I realized it was a skin ointment before I had squeezed any on to my toothbrush.  And it provoked the thoughts related to habit, creativity, evolution, and God.

HABIT

I do a lot of thinking in the shower.  The tasks of showering have become a nearly mindless routine.  Other physical tasks are put aside.  Conversation, reading, eating, TV, phone are impractical while showering.  So one is left with thinking as one of the few activities conveniently accompanying showering.  Unfortunately, thinking sometimes interferes with accomplishing the shower efficiently; for this reason it can be an ecological error wasting hot water although the time may be well spent if thoughts are productive.

The delay made me even later than I had planned to be for my youngest grandchild's final soccer game of the season.  The role of habit is enshrined in the aphorism "we are creatures of habit".

In sports and many other activities, we take advantage of habits by promoting them in an activity we call "practice".  The value there is three-fold.  Practice exercises and helps develop the muscles involved in the various movements of the practice.  Practice presumably enhances the performance of the nerve and synapse pathways used in the activity.  Those activities of the pathways may be induced by a simple stimulation of one neuron rather than the multitude of ones needed to be incorporated during the laborious learning period.

Many neural pathways are a result of normal development.  One of the more simple types is the knee jerk reflex when the patellar tendon is tapped causing lower leg extension without brain involvement (just a reflex arc involving at least a sensory neuron, an association neuron in the spinal cord, and a motor neuron) producing the muscular action.

EVOLUTION

Habits can be learned.  As noted in the previous section they can be beneficial.  Natural selection can result in improvement of animal features that enhance survival and reproduction.  Some consequences of such a selective line could be increased size of the nervous system, and thus possible adaptive variety in neural pathways.  Also increased/decreased size toward optimal size can evolve.

Aping
The natural tendency to mimic is seen in other primates as well as ourselves.  It certainly had a beneficial role in survival of ancestors.  One offshoot of aping is follow-the-leader.  It enabled activities and movements to be passed on from generation to generation before written and/or spoken language were available.  Would agriculture or migratory paths of nomads have been established without this tendency?

Sometimes negative habits of this type can be result from peer-pressure, like armies so dedicated to the leadership that they easily(?) do horrible things.  Or a dislike of broccoli may be produced by an inappropriately timed grimace on a parental face.  The same phenomenon may have saved countless ancestors from ingesting poisonous foods.

Instinct
Evolution via natural selection can help incorporate behavioral features that are hard-wired and/or enhanced by experience.  One well known example is the imprinting shown by geese studied by Lorenz.  The first large moving object they encountered after hatching was treated by the baby geese as mother goose.  If they saw Lorenz first, they followed him as goslings normally follow their mother.

Evolutionary steps of behavioral attributes
Behavioral attributes are probably at least as slow to evolve as are physical attributes.  One reason is that physical attributes are continuously exhibited in contrast to the occasional employment of a behavioral attribute.  I saw this with surprise when I heard a robin outside the laboratory when I was at the University of Tasmania.  I went to the door and saw an all black bird, robin sized, but without the familiar red breast of the North American robin.  Its tail flicks, hopping, and cocking its head to find a worm were identical to my experience with the robins at home.

Turdus turdus, the robin first described by Linnaeus is the one in Tasmania, was remarkably like Turdus migratoria, the North American robin.  They presumably had been separated from their common ancestor by several millions of years, yet behavioral/instinctive/learned(?) attributes were still intact.

Insects are remarkably complex in the range of behaviors exhibited by different species.  Many of their instinctive behaviors are most certainly a product of variant selection in development of the nervous system.

Some related species may keep similar reproductive behavior connected with changing pheromones as species evolve.  Some closely related moths respond to a blend of sex attractant chemical only slightly different in proportions than those of close relatives.  They may function, for example, as intermediate stages leading to completely different sex attractants in other lines of different species.

Speciation
Insect behavioral changes may go hand in hand with changes leading to new species if the behavior leads them consistently to different locations or extremes of reproductive behavioral traits.  Some time physical changes lead to physical incompatibility of reproductive structures comprising the "lock and key" genitalia of female and male individuals.  Once temporal, geographic, behavioral, or physical changes produce reproductive isolation, speciation can occur.

CREATIVITY

One might think that habits were enemies of creativity.  When creativity represents change competing with the status quo our social systems tending to favor it can reduce creativity to some extent.  But developing behaviors or mental functions compatible with creative activity should benefit creativity.  These aspects may be found in some past, and probably some future, posts.

GOD

Habits have a role in our relationship with God that can be good, bad, or of little importance.  The topic deserves more extensive treatment in a later post.  It may be good to have a habit of prayer, but don't be so hide bound by it that you do not react and rescue the little child in the path of the approaching train.  Or, don't be so charitable giving away your money if your family desperately needs it for food, shelter, or clothing.

Joseph G. Engemann    October 11, 2014

CREATIVITY

Reverse Viewing

THE TWO WAY STREET

My creativity manuscript, The Two Way Street, Chapter Five, begins with the sentence - "Seeing things from more than a single point of view is the fuel for creativity."  "There is no such thing as a one-way street; it is only usage that makes it so.  If there is no requirement that there be only one solution possible to a problem, there is no inherent logic that limits the possible solutions to two or more."

EVOLUTION

The answers to evolutionary questions have often been short-circuited by buying current fads and not looking for alternative solutions.  The fad may have some value in partial solutions, but can obstruct a view giving a more complete or accurate answer if we buy it as the total answer.  For example, catastrophism and inheritance of acquired characteristics were early views of little value beyond the historical aspect.  Embryological similarities and current limited DNA studies are of partial value but inadequate as currently applied in major phyla relationships.  A major focus of many other posts on this blog is presenting evidence to help straighten out the current mess in the view of higher phylum relationships.

PARTIAL TRUTHS

I am not immune to making errors, some basic ones, as well as some simple typos.  Misapplication of the theme of this post  and my fallibility is the theme of the cartoon below from chapter five.

The caption, "This thing should be slippery in either direction!", has an element of truth but isn't of much functional value without some force to counteract gravity.  But it does indicate how I can get carried away with an idea.

The final paragraph of the chapter

"This point is the essence of creativity, looking actively for another answer.  Examining all points of view; submerging our inherent self-centeredness to see answers emerging from other points; proceeding in other directions; such an approach with people can improve our relationships, the happiness of all concerned, and increase our creative potential.  It is the beginning of understanding and rapport to look for the other person's point of view.  If you have not done that but begin to do it, do not be discouraged if your action is not reciprocated.  Remember how long it took us to reach that point.  We must retain our breadth of view in all areas if we are not to let a self-limiting, self-serving view encroach on our creative potential."

[The quoted portions above were written in the early 1970's, about ten years before I had the "eureka" event seeing how the pogonophorans were the major link that had been missing for understanding the origin of deuterostomes from protostomes.]

CREATIVE ATTITUDES

Reverse viewing is one of several metal habits that can be useful in becoming more creative.  A questioning attitude, with a willingness to accept what we question if it is supported by the facts, is another way to break free from the "status quo" resistance to change common to our thinking.  Most change is bad in a well-designed system.  The chromosomal repair mechanism has evolved and generally does what's best.  But in our own thinking we need to evaluate proposed changes, as well as what is presently the case, in order to progress to an improved solution.  Look for what makes a seemingly erroneous view be endorsed by others.

So question, evaluate, search for solutions, be interested in the world around you, be humble, and be on your way to being creative.  Be convinced that there are causes for everything; it is easier to believe so and more convincing if you believe in an Ultimate Cause; it impedes looking for an answer if you think there may not be one.  Time is on your side.

Joseph G. Engemann     Kalamazoo, Michigan    October 6, 2014

EVOLUTION, SCIENCE AND EXTRATERRESTRIAL LIFE

Evolution, Science, and Extraterrestrial Life

EXTRATERRESTRIAL LIFE

The search for extraterrestrial life was featured in a NOVA, or some other, television program I happened across yesterday.  Over the years I have come to the conclusion that there are people on countless other planets in the universe, but that documenting or proving it is impossible.  Still, it is worth considering the arguments and evidence that might convince us of the existence of someone with a potential to communicate with us from some far galaxy.

SCIENCE

The most hopeful search described on television was an attempt to detect radio-wave transmissions from outer space via a reception on a radio-telescope array.  Radio-waves are presumably subject to no, or less, distortion as they travel through space and matter intervening in space.  The opportunity for success is infinitesimal, or so close to zero, that I doubt it is worth the effort for the following reasons.

1.  Pinpointing a source would be more difficult than spotting an ant on earth from a telescope on the moon.

2.  A potential source would likely be of short duration relative to the long time the signal would take to reach the earth.  Possible reception from pointing the radio-telescope at the right planet or star might also precede or follow the time a signal is generated.

3.  The algorithms and signals that brilliant minds are expected to develop and send my never be sent because they are even more intelligent and understand its impossibilities or lack of potential use for communication requiring many years between sending and receiving.

4.  The formation of galaxies, stars, planets, and the elements likely to produce a potential life inhabited planet happened many millions of time during the development of the universe.  But those millions are too isolated by time and space for even a slight chance of discovery.

EVOLUTION

Of the many billions of planets produced, millions have likely gone through an evolution of carbon-based life that could well have produced conditions needed for the evolution of life during some period in the past ten billion years.  It would have required several things.

1. The right blend of chemistry, temperature, radiation, gravity, and relative stability of conditions.

2. Sufficient time with those conditions.

The natural selection outcomes would result in evolution likely including some outcomes with

1. Biochemical features much as organisms on earth have.

2. A lot of systems similarity to earthly organisms.

3. Similar ecological roles for different groups of organisms.

4. Social structure, and greatest technological advance with an organism about the size of humans, probably bipedal; but perhaps with different numbers of digits and vertebrae.  They would probably dream about being able to fly like the little fliers and the big fliers of their worlds.

A big question, would the dominant organisms have pigment variations like us or would they all be green?

CREATIVITY

Silicon based versus carbon based life systems seem an interesting possibility in science fiction.

Some find the interacting whole of the biosphere is some type of organism; there are interesting parallels between biosphere and organism that are better explained by ecological principles.

GOD

God is probably amused by those people on planets to whom he* was willing to reveal himself* for their belief that they are the only ones of importance to him*.

* I don't think God has a struggle with our inability to come up with an agreed upon, non-gender based way of describing I AM. I AM, the creator of the universe and all that is in it as well as the underlying or embedded principles leading to the world and its ways.

Conclusion: extraterrestrial life probably exits in the present, probably existed in the past, and will probably exist in new places in the future.  We are unlikely to ever know for certain from physical evidence in our present state.


Joseph G. Engemann    Kalamazoo, Michigan    October 4, 2014

EVOLUTION: NUCLEOTIDE MUTATION RATES

Evolution: Nucleotide Mutation Rates

MOLECULAR CLOCKS

If nucleotide mutation rates were the same for all organism and all parts of the genome, they would be the basis for a perfect molecular clock to determine relationships for constructing evolutionary trees.  But they are neither the same for all organisms nor even for various portions of the genome for the same organism.

For those wishing a more comprehensive view of the variables, they may be found by searching for nucleotide mutation rates in Wikipedia, or elsewhere, on the internet.  To the best of my knowledge, my peers have neither found nor embraced the evidence I have presented in other posts on this blog showing the major errors in the current published articles on the relationships of phyla and the importance of the Pogonophora in demonstrating those relationships.

MUTATON RATE VARIABLES

Some variables are known but not considered in several major studies, thus producing major errors in proposed schemes of animal evolution.  A variation produced by different generation times is the major factor affecting rates of origin of phyla when extremely low evolutionary rates occur - as noted elsewhere in this blog for pogonophorans and perhaps nematodes.  Most variables would have a proportional affect within the variation caused by generation time.  Fortunately, the affect of generation time diminishes to near zero as one approaches the species level.

Variables

There are many documented studies showing different rates for different groups of species.

1. Viruses with RNA genomes mutate at a much faster rate than organisms with DNA genomes.

2. Mitochondrial DNA has a faster mutation rate than nuclear DNA.

3. Methylated DNA is more resistant to mutation than DNA that is not methylated, as in sperm which have higher mutation rates than eggs.  This is perhaps tied in with the fact that sperm genes may be expressed in the individual produced more than is expressed by genes from the egg.  Methylated DNA from the egg may also be a reason that dosage affect on gene expression has less impact than one might expect from comparison with instances where three of a particular chromosome are present.  The methylation effect is not total; that is shown by Medel's pea experiments where the flower pigment expressed is dosage dependent, and in humans where the sickle cell gene is less debilitating in the heterozygous condition.

4. Mutations are more likely to occur near sites where chromosomal deletion or insertions have occurred than in more distant locations from those mutated sites on the chromosome.

5. Genetic factors may affect rates; perhaps through variations in function of chromosomal damage repair functions.  Rates may be subject to natural selection balancing the value of introducing change versus the stability desired in successful genes.

6. Environmental factors such as variation in background radiation and/or the extremes of deep sea pressure  may also affect rates.

7. Generation time is the current source of error in relating major groupings of phyla.  This error is also a factor in proposals of a time of origin of humans relative to monkeys and great apes.  But it is not a factor in most studies of animals sharing the same species, genus, or family.  However it may be more of a factor as one compares orders and classes of animals.

A botanist colleague maintains generation time is not a factor in evolution of flowering plants, although I think that has yet to be proven.

Generation time versus age affects?

The question might be of interest in human evolution because older individuals may be more likely to have experienced mutations in germ cells, especially sperm, whereas eggs may be spared much of the generation time effect by all being produced before birth as well as by having methylated DNA.

I have not given much thought to this as a general factor because it does not seem apparent for animals in the deep sea that were critical in providing the clue of the annelid ancestry of chordates.  If long generation time corresponds with more mutations per individual, it would seem to cancel out to some extent the generation time effect in evolutionary rates.  The extreme difference of generation time of abyssal animals critical in the early origin of phyla makes cancellation of this type of little importance when considering overall evolutionary trees of the major groups of animals.

Natural selection

The rate of mutations may not have as much to do with evolution as does natural selection.  Beneficial mutations, although they are much rarer than other mutations, tend to be incorporated in the species gene pool via natural selection or survival and reproduction of the individuals having them.  Whereas deleterious mutations tend to be eliminated.  In mammalian species much of the genome is thought to be non-coding and in the regions of the chromosome between the genes or coding regions.  Mutations in the non-coding regions are thought to be of little consequence as long as they maintain the chromosomal integrity.

Although rates are not necessarily of major impact on the direction of evolution, they are essential to consider in establishing the branching pattern of evolutionary trees, especially as regard major group relationships.


Joseph G. Engemann    Emeritus professor of Biological Sciences, Western Michigan University  October 1, 2014