Friday, January 23, 2015

SALVAGING DATA FOR EVOLUTION STUDIES

MOLECULAR DATA

It occurred to me within the past day that I have ignored one of the things I learned in my youth - how to get some use out of discarded materials in the city dump!

Such experiences were something few children in modern cities get.  So many of the products we use are not designed to be repaired, just throw the whole thing away and get a new one, or at best, get a module to replace a portion.

So my criticism of the Ecdysozoa and Lophotrochozoa studies [post of May 31, 2013] overlooked the fact that, if the errors introduced by linking most ancient ancestors were taken in to consideration, and some such ancestors were omitted in a new analysis, the remaining data might lead us closer to the reality of the ancestral paths.  Even so, the inadequate sample sizes and the limited portion of the genomes examined are unlikely to be very useful.

I don't think it is worth trying because the sample sizes were already inadequate and might still be if clusters could be reanalyzed omitting the nematodes in the Ecdysozoa study.  Nematodes need omission not only because they may have extreme retention of genomic identity giving them "long-branch attraction" to diverse distantly related groups, but they also are a separate lineage that is not basal to any other major modern group.

The Lophotrochozoa represent newer evolutionary events.  Because uncertainty due to variable length of lineages from common ancestry of early coelomate animals, and the "long-branch attraction" problem affecting some of the members descended from annelids via the Pogonophora, the relationship of various "lophophorate" clusters can not be determined with simple corrections.

EMBRYOLOGICAL DATA

As discussed in my posts regarding isopod egg comparisons it is clear that the old idea of the "biogenetic law" where animals were thought to repeat some steps of their evolutionary development in their individual embryonic development is not valid.  But I hope I made it clear that the concept is still a useful model that may suggest investigation for support from other evidence.

The isopod eggs, and ecological factors involved in deep-sea selection, helped me see how the Pogonophora explain the close relationship of ancestry of deuterostomes to advanced protostomes.  Judging from the number of views of my blogs on the topics, I think people studying such things are unlikely to know about them and thus will be unable to apply the concepts.

ANATOMICAL DATA

Amazing data can be found in studies of anatomy.  But it is increasingly unlikely to be helpful, not because it can't be, but because modern researchers are swamped with so much useful information they will never get far into older studies and approaches.  Anatomy and its changes not only reflect evolutionary history but are intimately connected with the genomes of animals.

The environment imprints it natural selection role on structure, development, and the responsible genes.  But the complex interaction is so nebulous I pity the researchers of today who are certainly more technically advanced than I have ever been.  The day is not long enough, nor their life long enough, to have much chance of putting it all together.  Still, I anticipate the continuation of the string of remarkable advances science can make in many areas.  I hope they can still get the benefits study of the humanities can make in their lives.

Joseph G. Engemann    Kalamazoo, Michigan    January 23, 2015

Wednesday, January 21, 2015

OUR RELATIONSHIP WITH GOD

The Point of the Previous Post

I had hoped to indicate all religious views have some good in them.  Most of my early life only gave me exposure to Christians.  I heard many of the contentious views that separated denominations.  But when I talked with friends from those different denominations, it was difficult to find fundamental differences of importance.

CHRISTIANS

My Roman Catholic background included seeing anti-catholic sermons advertised on signs in front of churches.  Of course, I worried about them not having the true religion I had.  I'm sure some of they worried about me for the same reason.  Perhaps my first enlightenment came with a discussion with my best friend from grade school, Jack Rumohr.  He was well along with his preparation for becoming a Baptist minister who later spent many years as a missionary in Africa.  Like most Protestants, I don't think he shared my views of the Pope, the Blessed Virgin Mary, Apostolic Succession of the priesthood, and details of sacraments.  But fundamentals about God and faith in our salvation through Jesus Christ had only semantic differences.

In graduate school, discussions with Pierson VanAlten made me see that the difference between Christian Reformed views of predestination, and free will as seen from my point of view, seemed to hinge on minor differences in understanding and the words used.  During my two years in the army, another platoon member was Warren Wiles, a Pentacostal Minister and a good friend with whom the sincerity of belief in the action of the Holy Spirit in his life was without question.

NON-CHRISTIANS

Herbert Wolfson was a Jewish friend, also in the same platoon in the army.  We went together on a three day pass to Vienna and had to pass through the Russian occupied zone of Austria.  We didn't discuss religion, but he was a good and honorable man.  The only Jews, in the town of 4,000 where I grew up, were Abe Friedman and his wife.  I knew neither one, but my father knew him from his business and had a very good impression of him.

OUTSIDE JUDAO-CHRISTIAN TRADITIONS

While attending the University of Tasmania I lived in a boarding house where two others were university colleagues.  One was a graduate student from a Muslim university in India.  The other was my room-mate who was a Hindu and a professor from a different Indian university, he was researching the chromosomal make-up of certain primitive gymnosperms.  In the years since then, I have gotten to know more of both Hindu and Muslim faiths.  That happened in the years since I was in Tasmania.

In 1980 I spent a few weeks in Libya with other member's of Abubaker Swehli's doctoral committee.  We visited several oases in the Libyan portion of the Sahara Desert.  The hospitality of the people in desert oases was remarkable as they hosted mid-day meals for our group of strangers.  Apparently, part of the Mulsim tradition is taking travelers into their home for up to three days, but at the end of three days it is time to go.

At the time we were there one of Dr. Swehli's siblings was being married in Tripoli.  I attended one of the wedding events where the men walked from the Swehli house to the house of the other wedding partner.  It was something like the shiveree tradition accompanying weddings in the old American West.  I was not a vocal participant in the process, but one of the participants engaged me in conversation about his pilgrimage to Mecca.  He was wearing the gown of the color signifying he had made the visit to the Kaaba.  He told me of its significance and then surprised me with the question "what is your big message in life?"  He may have phrased it differently, but I struggled mentally and came up with something I had thought about a number of times in the past.  I told him something to the effect that "one shouldn't take criticisms from others personally, they are just trying to make themselves seem or feel better."  For a long time after that I wanted to ask people with printing on their T-shirts, "what is your big message in life?"

After my year in Tasmania, I had stayed on for a few months with a fellowship extension to help complete a year studying the isopods discussed in other posts.  I got back to Michigan just in time to attend my younger sister's wedding shown in the photograph below.


                In the Catholic church in my hometown and my sister's wedding.

Now, after being fortunate to be friendly with people of many countries and of many religious persuasions, as well as some agnostics and atheists, I see why God is so happy with his creation and I should join my Protestant friends holding up the sign that says "John 3,16".  The message should make each person realize the vast amount of love God has for each one of us.

I am optimistic that the world is improving in spite of all the trouble and woe.  One bit of evidence is the first sentence of the prayer of Pope Francis for the month of January, "Dear Heavenly Father,
During this month we pray that you bless all those from diverse religious traditions and all people of good will, that they may work together to produce real peace in our world."

So what is our relationship with God?  God loves us.  Do we reciprocate that love as best we can?  It's never to late to start.  One way is to love everyone else; God does.  At least, smile once in a while, it's a start.

Joseph Engemann    Kalamazoo, Michigan    January 21, 2015

Monday, January 19, 2015

GOD and Religious Traditions

MONOTHEISM, belief in one God

Most people probably grow up thinking their religious tradition is the correct one favored by God.  Before the predominate view of a single, all-powerful, infinite God beginning with the monotheistic God traced back to Abraham, there were undoubtedly numerous traditions around the world.  Both Christians and Muslims trace their origins through, and, along with Judaism, back to Abraham or Abram about 4,000 years ago.

POLYTHEISM, belief in many gods

Polytheism was common in much of the world during pre-Christian times

The Hindu tradition began with a blending of the beliefs of new arrivals to India and those of native Indians about 3500 years ago, almost as early as Judaism began.  They are not far from monotheism by viewing the many gods as representing one divine principle.  Within Hinduism, Budda (Sidhartha Gautama) founded Buddhism over 2400 years ago.  Both Hinduism and Buddhism recognize successive reincarnation as aspects of their traditions.


The steeple of the Hindu temple above in Colombo, Sri Lanka, depicts many gods sculptured on it.

Confucius founded Confucianism in China over 2400 year ago.  A few generations later, Aristotle, a Greek philosopher and scientist, proposed his proofs for the existence of one supreme God.

My first roommate in a dormitory at Michigan State University, during my first year of graduate school, in 1954, was Toshiaki Kinjo, from Okinawa, Japan.  I didn't discuss religion with him much, but he presumably had a Shinto background.  He was one of the finest persons I have ever met.  I lost contact with him after he moved to Brazil to help develop agriculture in new areas.

ISLAM

Islam was founded by the Prophet, Mohammed, about 1400 years ago.  He recognized Jesus as a Prophet, but did not get the message that his divine nature as the Son preexisted in the one God, along with the Father and the Holy Spirit, as recognized as the three persons making up the One, Trinitarian God of Christians.  For Muslims, the first principle of their faith is declaring that there is one and only one God at least once publicly during their life.


                                Mohammed Ali Mosque (back, right) in Cairo, Egypt

Their second duty is to pray at least five times throughout the day.  One or more minnerettes (or towers on their mosques) are used to call the faithful to prayer at appropriate times.  During prayers, they face the Kaaba, located in Mecca, Saudi Arabia.


                      A minerette viewed from a balcony of a mosque in Bombay, India

Muslim duties also include paying alms, fasting during Ramadan, and, if possible, making a pilgrimage to the Kaaba at least once during their life.  Like other religions, Islam has versions, about 90 percent of Muslims are Sunni, about ten percent are Shiites of one of three groups.

THE GOLDEN RULE

All major religions preach some form of the Golden Rule as being part of their moral code.  Treating others as you want to be treated is usually a good idea.  But apply it reasonably and don't force candy on a diabetic.  In fact, don't force anything on others and be cautious about applying a right of self-defense.  Freedom and slavery issues have plagued humanity from inherited built-in survival mechanisms developed earlier in our evolutionary history.

TERRORISM

Violence seems to have been something religions have not escaped.  Fanaticism of some divine right or obligation may possible be derived from some aspects of Old Testament theology.  In its worst form in recent years, such as the dictatorships leading up to World War I, it was not particularly religion based.  But, much earlier, the Crusades and the Inquisition had religious roots.  Today, the Islamic world, over one and a half billion strong, is embarrassed by the small fraction with mostly Shiite background trying to avenge perceived wrongs.  The Christian embarrassment has not ended with the Inquisition; witness the activities of the Ku Klux Klan in the United States and the attempts of the Irish to solve their political problems.  Of course terrorism, partially religion based, in several African countries has yet to be solved.

HOW DOES GOD VIEW RELIGION?

Looking at where God's Son took on human form in the person of Jesus might shed some light on the question.  Muslims came after the fact, and Judaism was the smallest of the three great traditions of the time.  That part of the world was frequently beset with wars, invasion, plundering, and placing the conquered into slavery.  Perhaps the Oriental and Indian regions, especially in China, had similar turmoils but fairly stable and peaceful times seem to develop.  Although I am largely ignorant of the history of the Eastern part of the world, it seems that the family had developed into a stable unit, and older family members were accorded great respect.  Deceased ancestors were also viewed as being an important part of their heritage.

So Jesus went where he was sent and needed.  In the process he fulfilled predictions of the prophets, becoming the greatest Jew and prophet or rabbi the world will ever see.  He charged his follows to carry his message of love and redemption to the rest of the world.

So the message that Jesus left us with that God loves all of his creation and knows our inmost thoughts, may indicate the following.  The peaceful orient already understood the message, but the warring Middle Easterners needed more direct instruction.  His criticism of the priestly leaders style of not following what they were preaching can probably still be seen as needed.  Hence the hope engendered by the comments of Pope Francis to the Curia.  Perhaps such problems leave Protestants relieved they need no top human leader.  I suppose Imams having different views of Sharia may be less of a problem if they do not have civil authority combined with their religious role.  Separation of church and state seems a good principle to follow.

So, you can see I don't really know the answer to the question.  But my having had the benefit of knowing Christians of many persuasions, as well as Jews, Muslims, and Hindus makes it easy to see that God loves all the people he has created. And that includes agnostics and atheists.  Maybe some are special, but Jesus said "in my Father's house are many mansions" and "others I have that are not of this fold".  In fact, all individuals are special; God not only knows us better than we do ourselves, he also loves us more than we do ourselves.  That love extends to forgiving us all our failings if we turn to him.


Joseph G. Engemann    Kalamazoo, Michigan      January 19, 2015


Wednesday, January 7, 2015

ICE STORMS

The Beauty of an Ice Storm


                                                      is often not appreciated.

The picture above was taken in January over thirty years ago of fruits on a small tree beside our house.  Before the winter was over the berries were eaten by a flock of birds whose usual food had become snow covered or eaten.

In the spring, well after the ice storm, I looked up and saw slashes of light colored wood on the upper branches of big silver maple trees along the street.  Throughout the city there had been many trees and large limbs broken down by the load of ice the trees bore.  A coating of ice on the tips of upper branches presumably broke off many of the small upper twigs and lightened the load on the big branches so most trees survived.

About a dozen years ago we were in a different house when another ice storm hit.  The most remarkable damage in our yard was a tall pine tree in a neighboring lot broke off and almost reached our house.  I had noticed that the upper part was bending over under the weight of ice and better exposed the branches to more freezing rain and ice accumulation.  During the night the trunk snapped off about ten feet above the ground.

The consequences of such events must have a selective role in the lives of many organisms.  In a forest the occasional large tree falls and leaves an opening for sunlight to enable a new cycle of plant growth near the ground.  The various plants have a role in feeding or hiding animals from small to big.  Such complexities have no doubt been a feature of the environment organisms adapt to over time as they evolve to better compete.  If they don't they join the throng of extinct species preceding them.

There are many natural disasters that do have a role in natural selection even though they arrive at unpredictable intervals and locations.  Many of the disruptions we cause may affect the course of evolution, sometimes in ways similar to natural disasters, sometimes in ways that may be worse.

Joe Engemann       Kalamazoo, MI      January 7, 2015

Saturday, December 27, 2014

Konnersreuth

KONNERSREUTH AND TERESA NEUMANN

Konnersreuth is a small Bavarian town and the home of Teresa Neumann.  I visited the farming town of about 1,000 people because I had heard of the stigmatic, Teresa Neumann, from my mother and somehow remembered it while I was stationed in Germany in 1952,  It is amazing that Ed Klem and I could find a bus from near our Grafenwohr maneuvers site to where we got of the bus and walked down the road to Konnersreuth, passing a farm with a team of bullocks.


Entering Konnersreuth

As we entered the town, one of the first houses on the left had a small shrine in the garden next to the house of Teresa Neumann.  

The house was home to the Neumann family and their ten children, Teresa was the oldest and born in 1898.  The streets of town were almost deserted, and Ed and I seemed to be the only tourists.  I don't remember now, 62 years later, if we found a place to have lunch or how we learned that it was Teresa's home.


According to an account in The Two Stigmatists PADRE PIO and TERESA NEUMANN  by Charles M. Carty, which I bought in 1959, the Neumanns farmed, but the farming was mostly done by the mother because the father also worked as a tailor to supplement their income.  Teresa also helped with the farm work.  The caption in the book, of a black and white photo of the trellised end of the home, noted that Teresa's bedroom was in the upper level of the home.

Her church, the steeple of which is visible in the first photo, was a short way from the home.  A second picture of two very similar ones was selected because it had someone in it as seen below.


Inside the church, the view toward the main altar shows no one.  But while we were in the church a lady, dressed in predominately black clothes, may have been Teresa Neumann as she was attending to some tasks in the altar end of the church.  I suspect it was her because she was wearing black gloves, perhaps to cover up the stigmata on her hands, or perhaps the church was unheated.


We departed without disturbing her and somehow managed to get back before the bus went back to Regensburg, or wherever it was that we could get transportation back to the Grafenwohr maneuvers area.

STIGMATICS

Stigmatics are individuals that typically bear a wound on each hand and each foot at points where Christ was impaled with nails to the cross as well as one on the side where the soldier's lance pierced him.  The wounds usually bleed on Fridays and especially so on the Friday commemorating the Crucifixion.  In Teresa Neumann's case, she also had a wound on the shoulder corresponding to the effects Christ had carrying the cross for his crucifixion in addition to numerous smaller ones from a crown of thorns.

Teresa Neumann is reported to have received the stigmata in 1926 shortly after she was miraculously cured from a series of different health problems for the sixth time in three years after praying for St. Teresa of Lisieux's intercession.  Several spiritual gifts usually accompany the stigmata, one most of us would understand is the gift of healing.  One that was intensely investigated was her regaining her weight after losing much blood each Friday but only eating a wafer of eucharistic bread each day and not drinking water for most of the 31 years up to the time of publication of the book mentioned above.  

Teresa Neumann died in 1962.  Carty quotes from Konnersreuth Today, (1950) by Frohlich, as Teresa responding to a fundamental question of life about the meaning of suffering with "The voluntary assumption of suffering in the spirit of atonement and expiation is an heroic act of love of God and profits one's neighbor's."


Joe Engemann     Kalamazoo, MI     December 27, 2014

Friday, December 12, 2014

OUR LINEAGE EXPLAINED

OUR EVOLUTIONARY LINEAGE

The preceding post of December 8, 2014 gives a condensed version of the evolutionary line listing 25 groups going backward from humans to an early animal group, the amoeboflagellates.  The list ignores the many other lines of evolution leading to other existing groups of animals such as echinoderms, mollusks, arthropods, and classes of annelids other than the polychaetes.  The polychaetes also are the earliest common ancestor of those groups as well as of all vertebrate groups.

The time scale of our ancestral tree follows the 25 groups of the first listing, but in reverse order with some additional steps beginning with the creation of elements and three other pre-biotic events not well covered in earlier posts.  The elements were formed in a second or later generation of stars preceding our sun.  They provided the material that eventually produced the more complex molecules from which living systems evolved on earth.

Those complex molecules formed from various processes as the earth cooled and the oceans formed.  Carbon dioxide, ammonia, water, methane, and various minerals were the materials acted upon by heat, radiation, and lightening to produce amino acids and other compounds.  Chance interactions of those compounds were probably enhanced by concentration in tidal pools.  There the mixing by waves may have utilized not only products produced by adhesion to various rocks, but compounds imported by water currents from remote locations.  One of those locations could well be the thermal vent areas proposed by Corliss as a place were life originated.  But similar processes could have been enhanced at inter-tidal locations as lava flows entered the sea or at other volcanic locations.

Following the four pre-biotic steps are five steps leading to the choanoflagellates, the ancestral group from which all animals arose.  Plants presumably are derived from earlier flagellated ancestors.  The remaining steps as well as the preceding steps are only cameos along a continuum of populations of organisms usually much like their closest ancestors and descendants.

Ten steps from sponges to the first chordates took about a billion years to occur.  The preceding evolution of living organisms took almost twice as long.  From the earliest, almost worm-like, chordates to us took a little over a half-billion year.  About eighty percent of that time was taken to produce the first primates.  It is likely our ancestral line never included a monkey that could hang from its tail as some South American monkeys can.

I mentioned the later because a monkey, if it could philosophize, might pity us for having lost our tail.  Likewise, the course of evolution includes many steps that might be considered regressive, but ones enabling later advances.  One of the most prominent, but least known, of such type event is the reduction of systems suffered during the evolution of polychaete ancestors to our pogonophoran ancestors.

Joseph Engemann     December 12, 2014

Tuesday, December 9, 2014

OUR EVOLUTIONARY LINEAGE

OUR ANCESTRAL TREE

From several chapters of my 2010 unpublished manuscript, Evolution Insights, I have pieced together the following direct lineage leading back to our protozoan ancestors.  Within the groups listed were many other groups ancestral to side branches making up an evolutionary tree of life.  Implied for the lineages within each group is a vast continuum of extinct species from those much as in the preceding or subsequent phyla or groups named.

CHORDATA
                                          Humans
                                          Hominoids
                                          Monkeys
                                          Primitive Primates [extinct]
                                          Insectivorus mammals
                                          Early mammals [extinct]
                                          Therapsid reptiles [extinct]
                                          Stem reptiles [extinct]
                                          Labrinthodont amphibians [extinct]
                                          Crossopterygian fishes
                                          Jawed fishes
                                          Agnatha
                                          Cephalochordata
HEMICHORDATA           Hemichordata
ANNELIDA                      Pogonophora
                                          Polycheata
[hypothetical]                     [Protonemertean][extinct]
PLATYHELMINTHES     Triclad turbellarian
CNIDARIA                       Hydrozoans
                                          Tetracorals [extinct]
                                          Tabulate corals [extinct]
PORIFERA                       Sclerosponges
                                          Simple sponges
PROTISTA                       Choanoflagellates
PROTOZOA                    Amoeboflagellates

A Time Scale of events associated with the above transition in reverse order beginning with the formation of elements in the universe follows the first seven below.  [bya = origin in billion of years ago;  mya = origin in millions of years ago]

Item or adaptation       -       Origin       -       Group

Elements                               > 12 bya
Ammonia, water, methane     > 4 bya
Amino acids, small organic molecules    ~ 4 bya
RNA, DNA, organic membranes          ~ 4 bya

Early cells    -     ~ 3.5 bya      -                bacteria
Photosynthesis     -     ~ 2.5 bya    -       photosynthetic bacteria
Chromosomes, nucleus, sex     -     ~ 2 bya     -     amoeboid protozoans
Cells with mitochondria and flagella    -    < 2 bya    -    amoebas, flagellates
Amoeboid and flagellated cells in colonies -  ~ 1.5 bya  -  Choanoflagellates

Extracellular skeletal fibers, spicules  -  < 1.5 bya   -   Porifera (sponges)
Sponges with massive carbonate base   -      < 1.5 bya   -    Sclerospongea
Nerves, muscles, gut      -     ~ 1 bya    -     Anthozoa
Manubrium, rhopalium     -    ~ 1 bya    -    Hydrozoa
Head, bilateral symmetry, sex organs   -    ~ 1 bya   -    Triclad flatworm
Blood vessels, anus     -       ~ 1 bya    -   [protonemertean]
Segmentation/metamerism, nephridia   -  ~ 1 bya  -  Polychaete annelids
Loss of segments, gut, & spiral cleavage    -    ~ 1 bya   -    Pogonophora
Gut restored, gill slits     -     < 1 bya     -      Hemichordates
Notochord    -    ~ 0.5 bya    -    Cephalochordates (first chordates)

Cartilaginous skeleton, vertebrae     -     ~ 0.5 bya    -       Agnatha
Jawed fish, bony skeleton     -      > 400 mya    
Lungs, fleshy fins          -       > 400 mya     -      lungfish
Four fleshy fins      -    ~ 400 mya      -      -     crossopterygians
Four bony legs, three chambered heart    -    ~ 400 mya    -      amphibians
Shelled egg, internal fertilization      -     ~ 300 mya    -     reptiles
Hair, large brain, warm-blooded     -     ~ 200 mya    -    mammals
Arboreal insect eaters, clawed   -   ~ 150 mya   -   insectivorous mammals

Arboreal fruit eaters, nails     -     ~ 70 mya     -     primates
Large size and brain, loss of tail    -     ~ 40 mya    -    apes
Upright posture, brain volume increases   -    ~ 20 mya      -   hominoids
Primitive humans, still larger brains     -    ~ 4 mya    -    Australopithecus
Modern humans, brain doubles  -  > 40,000 B.C.  -  Homo sapiens

    [protonemertean] is a suggested line of near relatives of nemerteans

The polychaetes were the protostomes that gave rise to deuterostomes through the Pogonophora as discussed in previous posts of last year.
The polychaetes also gave rise to all the advanced protostomes such as arthropods and mollusks through other lineages not shown here (see earlier posts on arthropods and mollusks).

The view above is at odds with the mistaken impression in recent literature which accepts two erroneous groups, including one that places nematodes in an untenable ancestral position for several phyla.  The mainstream position of sponges is seldom recognized nor is the simple transition from sponges to cnidarians to flatworms then nemerteans.  I expect my peers will be unable to comprehend the above until they grasp the extreme longevity of deep sea ancestors.  I take sole responsibility for any errors in these comments and tend to leave off my title of Emeritus Professor of Biological Sciences, Western Michigan University, Kalamazoo, Michigan - to avoid being a source of embarrassment for such a fine institution and for those who were my students.

Joseph G. Engemann           December 9, 2014