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




Tuesday, November 25, 2014

EVOLUTION: MOLECULAR CLOCKS

MOLECULAR CLOCKS AND EVOLUTION

Here are a few copied and pasted annotated references, from a file of references on the computer I currently use, that may help show the validity of my 6th post – Science Screw-up No. 1 – posted May 31, 2013.  I shudder when I think how many others were lost in various ways from the overwhelming amount of literature on the topics that interested me enough to make index cards, entries on earlier computers, and stacks of journals and clippings still unpacked from moves.  Some were cited in the post noted above, but lacked the annotations and/or quotes from the articles.

Because structure and functions of organisms are the direct targets of natural selection they can be a better clue to branching pattern of the tree of life until the generation time of organisms is properly incorporated in the process of tree construction.  Many of my posts rely on this concept for interpreting relationships as well as the views of natural history oriented biologists.

MOLECULAR CLOCK VARIABLES

Ayala, Francisco J.  1997.  Vagaries of the molecular clock.  Proc. Natl. Acad. Sci. USA, 94:7776-7783.  Found as much as a ten-fold difference between divergence times estimated by two different Drosophila genes (GPDH and SOD, or, glycerol-3-phosphate dehydrogenase and super oxide dismutase).  Generation times were identical in this study so did not affect the rate variation determined.

Bleiweiss, Robert.  1998.  Slow rate of molecular evolution in high-elevation hummingbirds.  Proc. Natl. Acad. Sci. USA, 95:612-616.  “A slower rate of single-copy DNA change at higher elevations suggests that the dynamics of molecular evolution cannot be separated from the environmental context.” The effect remained “significant even after taking into account a significant negative association between body mass and molecular rate.”

Britten, Roy J.  1986.  Rates of DNA sequence evolution differ between taxonomic groups.  Science, 231:1393-1398.  “Examination of available measurements shows that rates of DNA change of different phylogenetic groups differ by a factor of 5.  The slowest rates are observed for some higher primates and..”
 
Buckley, Thomas R., Chris Simon, and Geoffrey K. Chambers.  2001.  Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support.  Syst. Biol., 50(1):67-86.  variation in variability across data sets changes estimates, under different model assumptions, of nodal support and branch length   

Campbell, J. H.  1987.  The New Gene and Its Evolution.  Pp. 283-309 in Campbell, K. S. W., and M. F. Day (Eds.).  Rates of Evolution.  Allen and Unwin, London.  314 pp.  Rates of evolution pp 303- “To the extent that biological mechanisms participate in evolutionary change they allow its rate to be programmed internally as an attribute of the species.”

 Clegg, Michael T., Michael P. Cummings, and Mary L. Durbin.  1997.  The evolution of plant nuclear genes.  Proc. Natl. Acad. Sci. USA, 94:7791-7798.  “Analyses of synonymous nucleotide substitution rates for Adh genes in monocots reject a linear relationship with clock time.”  New genes that encode the enzymes ribulose-1,5-biphosphate carboxylase and alcohol dehydrogenases occurred at ten times the rate of new genes for alcohol dehydrogenases.    

Denver, Dee R., Krystalynne Morris, Michael Lynch, Larissa L. Vassilieva, W. Kelley Thomas.  2000.  High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegansScience, 289:2342-2344.  generation time of 4 days, used 74 lines of single worms, analyzed base pairs for mutations; 9.7 x 10 to the minus 8 per site per generation or 8.9 per site per million years.  “ . . . revealed a mutation rate that is two orders of magnitude higher than previous indirect estimates,”

Field, Katharine G., Gary J. Olsen, David J. Lane, Stephen J. Giovannoni, Michael T. Ghiselin, Elizabeth C. Raff, Norman R. Pace, and Rudolf A. Raff.  1988.  Molecular phylogeny of the animal kingdom.  Science, 239:748-753.  “Coelomates are thus monophyletic, and they radiated rapidly into four groups: chordates, echinoderms, arthropods, and eucoelomate protostomes.”  “The use of cellular RNA for these studies guarantees that sequences will represent commonly transcribed RNA genes, not minor or inactive genes.  The method provides sequences in the most conservative portions of the 18S rRNA molecule, which are the most useful for broad phylogenetic comparisons.” see following sentence page 748 also [“For distantly related organisms, it is not possible to establish homology between nucleotides in the rapidly evolving portions of the molecule; thus, even if the entire 18s rRNA sequence is known, only some parts of it can be used for phylogenetic inference.”].  Study was based on 18S ribosomal RNA sequences. Pogonophoran used was a thermal-vent species, annelids were a polychaete and an earthworm, chordates were a tunicate, amphioxus, a frog, and a human.

Fitch, Walter M., Robin M. Bush, Catherine A. Bender, and Nancy J. Cox.  1997.  Long term trends in the evolution of H(3) HA1 human influenza type A.  Proc. Natl. Acad. Sci. USA, 94:7712-7718.  Variation of replacement substitution rate of codons as much 7.2 times greater in a hypervariable one.  Rate lowest in trunk codons, intermediate in twigs, and greatest in tip branches.  [thought added 2/6/03 – might be an expression of selection against deleterious substitutions eliminated more effectively due to time as one goes to older twigs and trunk. (jge) I had just been thinking of that while trying to improve on method of calibrating molecular clocks with generation time corrections for both calibration species (if not from lines studied) and generation time difference of branch species (A correction of up to 199.999% of uncorrected bifurcation value is needed if generation time of shortest lived species was used; whereas estimate could need reduction of up to 99.999% if based on longest lived species); therefore two separate generations time corrections must be considered if calibration species is a third species; no correction for generation time is needed if all three have same generation time.]

Gillooly, James F., Andrew P. Allen, Geoffrey B. West, and James H. Brown.  2005.  The rate of DNA evolution: effects of body size and temperature on the molecular clock.  Proc. Natl. Acad. Sci. USA, 102:140-145.  support a single molecular clock, “but that it “ticks” at a constant substitution rate per unit of mass-specific metabolic energy rather than per unit of time.”

Keightley, Peter D., and Adam Eyre-Walker.  2000.  Deleterious mutations and the evolution of sex.  Science, 290:331-333.  [13 Oct 2000]  Deleterious mutations were eliminated more rapidly in short generation time species.  The study did not support (MD) “mutational deterministic” hypothesis for obligate sexuality.

Kimura, Motoo, and Tomoko Ohta.  1971. On the rate of molecular evolution.  J. Molec. Evolution, 1:1-17. citing various sources for a rate of about one centipauling for histones to four paulings for Fibrinopeptide A.  (1 pauling = “rate of substitution of 10 [to minus 9] per amino acid site per year.)

Kuman, Sudhir, and S. Blair Hedges.  1998.  A molecular timescale for vertebrate evolution.  Nature, 392:917-920.  [30 Apr 1998]  In estimates of divergence times using different genes, a standard error of about 10% was found using ten genes, but the standard error was only 5% if 50 genes were used and 3% with use of 100 genes.  Their study used 658 genes distributed among 207 species of vertebrates (mostly mammals).  [note added 11/25, 2014 -  this shows the ability of statistical analysis to give a more precise wrong answer, if a uniform rate premise is wrong – a point of my May 31, 2013 post; see Maley and Marshall, 1998 below also]

Laird, Charles D., Betty L. McConaughy, and Brian J. McCarthy.  1969.  Rate of fixation of nucleotide substitutions in evolution.  Nature, 224:149-154. a ten-fold higher rate of nucleotide sequence variation for rodents compared to artiodactyls is found when time estimates are in years  “This difference diminishes if generations, rather than years, represent the appropriate interval of evolutionary divergence.”

Maley, Laura E., and Charles R. Marshall.  1998.  The coming of age of molecular systematics.  Science, 279:505-506.  “Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally thought.” . . .  “In extreme cases the inferred relationships between groups may change when different representative species are used.” . . “as the amount of data analyzed increases, so does the apparent statistical support for an incorrect phylogenetic tree.”

Mishmar, Dan, Eduardo Ruiz-Pesini, Pawel Golik, Vincent Macaulay, Andrew G. Clark, Seyed Hosseini, Martin Brandon, Kirk Easley, Estella Chen, Michael D. Brown, Rem I. Sukernik, Antonel Olckers, and Douglas C. Wallace.  2003.  Natural selection shaped regional mtDNA variation in humans.  Proc. Nat. Acad. Sci. USA, 100(1):171-176.  p. 171-“multiple amino acid changes found in ATP6, cytochrome b, and cytochrome oxidase I appeared to be functionally significant.  From these analyses we conclude that selection may have played a role in shaping human regional mtDNA variation and that one of the selective influences was climate.”  P. 176 –“If selection has played an important role in the human mtDNA lineages, then the rate of mtDNA molecular clock may not have been constant throughout human history.  If this is the case, then conjectures about the timing of human migrations may need to be reassessed.” 

Miyamoto, Michael M., Jerry L. Slightom, and Morris Goodman.  1987.  Phylogenetic relations of humans and African apes from DNA sequences in the ψη-globin region.  Science, 238:369-373.  “. . the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans.” 

Mooers, Arne Ø., and Edward C. Holmes.  2000.  The evolution of base composition and phylogenetic inference.  Trends in Ecology and Evolution (TREE), 15(9):365-369. “. . , in the early 1990s, phylogeneticists discovered that the variation in GC content among organisms could wreak havoc on attempts to reconstruct evolutionary history.  This was because the tree-building techniques then in use often grouped together unrelated species with similar GC content.” 

Nichols, Richard.  2001.  Gene trees and species trees are not the same.  Trends in Ecology and Evolution (TREE), 16(7):358-364.  different genes may evolve at different points in time in the same lineage giving different times of separation if only one is considered to calculate divergence time

Shaw, Kerry L.  2002.  Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets.  Proc. Natl. Acad. Sci. USA, 99:16122-16127.  “The discrepancy between mtDNA and nDNA phylogenies reveals that speciation histories based on mtDNA alone can be extensively misleading.”


Simmonds, P., and D. B. Smith.  1999.  Structural constraints on RNA virus evolution.  Journal of Virology, 73(7):5787-5794.  Evidence of rate of mutations variation with nucleotide location in relation to secondary structure of GB virus C.  In this case, molecular clock assumptions are incorrect.  

Joseph Engemann    Kalamazoo, Michigan   November 25, 2014

Wednesday, November 19, 2014

CREATIVITY: FRAME OF MIND

Preparation for creativity

A dilemma is presented by the broad and deep background that is desirable for creativity - it can be an impediment to an unbiased view and preoccupy us with thinking that has not produced a solution. "A fresh approach is then more difficult than it would be for an intelligent, ignorant neophyte."

If you come up with a good idea without having studied the subject intensively, you won't know whether it has been done before or if some evidence exists showing it is impractical.  A second approach can be useful to both expert and neophyte, the development of a questioning attitude.

Questioning attitude

"A questioning attitude must be balanced with a confidence in the existence of solutions, answers, and causality.  Rather than let knowledge of an uncertainty principle escape its bound of valid application and erode our confidence in areas it has no application, we should focus on the universal relationship of cause and effect.  For every question, there is an answer, if only that the question is nonsense.  A questioning attitude can dampen the free flow of ideas.  Negative expressions are wisely excluded from group brainstorming sessions in the initial proposal developing stage.  Realistic evaluation comes later."

So, a questioning attitude, keep it reasonable.  The following cartoon may apply.

The caption says "Have you noticed how he never seems to agree when you say 'nice day'"

"Our minds can become channelized by factors other than the knowledge of literature and accomplishments in the subject.  Just as we use repetition to learn and fix things in our mind, repetition will make the implausible seem axiomatic.  This is a special danger to those ignorant of the the subject and in the favorable position of viewing it freshly.  The first idea, unless readily disproved, has the greatest chance of being repeated.  Succeeding ones have progressively less chance of taking the favored position.  Perhaps some people cherish their own idea because it is their only one."

The cartoon below speaks to the subject.

The caption says "Tell me it's not cancer doc, I've been worried ever since I got this persistent pain in my posterior."

"It is worth attempting a little self analysis to determine our personal quirks so we can compensate for them.  Do we reject the new?  Do we overvalue and revere the new experience just because it is new?  Is the old outmoded?  Is the old the proven best?  Do we delight in complexity, or simplicity?  Can we answer always to any of the preceding? If so we may have a built in bias toward or away from some ideas.  The hypochondriac, those with special fears, and those with special love do.  Don't we all?"

Honesty

"Honesty is essential to the maintenance of creativity.  Honesty with others will reduce self-deception.  Honesty does not mean that everything known must be used or told."

The cartoon for this subject follows.

 The caption says "I wish what went in Pat's ear went out the other ear instead of the mouth!"


Quotes and cartoons are from Chapter 4 of my unpublished 1974 manuscript, "The Two Way Street: One Approach to Creativity"

Joseph G. Engemann    Kalamazoo, Michigan     November 19, 2014

Monday, November 17, 2014

GOD: WOMEN PRIESTS?

CBS 60 MINUTES, November 16, 2014

A young reporter became a little more penetrating in her questions of Cardinal Sean O'Malley, Archbishop of Boston and presumably an adviser of Pope Francis, after some comfortable questions about progress in dealing with Vatican problems.  She did not seem satisfied with his assertion of a greater role for women and an existing high position of esteem for women in the church.

There may be practical reasons for not having women priests at this time, but the role of women and their relationship to Jesus was more extensive than seems consistent with the operation of society at that time.  Having only men among the twelve apostles closest to him was simpler than fighting societal norms of the time.  So the notion of Pope Benedict that relativism should be rejected, in favor of objective truth in moral and/or ethical decisions or their rules or guidance, could apply to favor women priests.  In the United States and many other countries women are taking their rightful place in society.  Unfortunately, not all countries offer them that role.

The church has enough problems with many celibate clergy having difficulty handling their role gracefully.  Add women to the mix - would that solve or exacerbate the problems?  I one time thought it would be a good idea to direct homosexual males into the priesthood; in my mind they had a reputation of being gentler, more social, and almost devoid of macho tendencies.  I think the past problems of pedophiles in the priesthood may be a separate problem of heterosexuals perpetuating the behavior they were victimized by as children.

The reporter said or implied that women were being discriminated against and denied a right.  But it is not anybodies right to be a priest.  I thought priests were special when I was a child.  I still think so, but now I know they are human and probably as prone to failure as anyone.  I was upset in early high school when a classmate informed me that a priest in a nearby country parish had a drinking problem.  It was later confirmed by reliable sources and may have helped me get a better sense of reality.  But people still expect more of the clergy and rightly so.

The church gets enough bad press without having to deal with unplanned pregnancies of clergy, remodeling rectories when the next pastor is a different sex, and the minds and actions of members unable to accept change.

Change can be good or bad.  It is good to challenge the status quo.  But change for change's sake is more likely to be a mistake in a well tuned system.  That is the principle we can get from evolution by means of natural selection.  But it also indicates changes that fine tune the system can be worthwhile.  I don't think voting on it is necessarily wise.  I hope the Pope is in a better position to wisely make that decision.  But now can 60 Minutes find out the chances of the next Dali Lama being a woman?

About twenty years ago I sent a long letter to Pope John Paul listing all the scriptural and other reasons I thought ordaining women was appropriate.  I doubt if the letter every reached him, but I had enough postage on it.  About ten years ago I wrote another letter to a pope about the compatibility of evolution and religion when some catholic publications were printing anti-evolutionary views, but I never mailed it.  Now it is evident the pope does not need it [see post of October 31].

Joseph Engemann       November 17, 2014


Thursday, November 6, 2014

EVOLUTION AND MARINE SEDIMENTS

MISH-MASH


Mish-mash is a title to accommodate comments with varied connections to the four main pages of this blog.   As may be evident from earlier posts, I am not as reluctant as I should be to talk about things I am not particularly well qualified to talk about.

Evolution, Invertebrates, And The Deep Sea 


Prior to the early 1980's it occurred to me that the conditions of much of the ocean bottom were so stable that a record of unusual disturbances is preserved for a long time in many locations.  Major disturbances show as unconformaties in rocks between periods of greater stability of deposition rates.  A study of deposition as it happens today makes interpretation of fossil deposition easier.  The gradual change in features of microfossils seems to be the rule when sediments are added without major disturbances such as those that characterize gaps separating major geologic times.  Disturbances were frequent enough during the sediment accumulation process that there is often a gap where transitional forms are not present; the concept of punctuated equilibrium is probably an artifact of those missing transitional sediments.  The opposite effect can be produced by action of bottom dwelling organisms or wave action mixing sediment above and below a gap and blurring the estimate of time of existence of a group.

Forams

A particularly useful group for dating sediments and seeing changes is the protozoan group known as the foraminiferans.  Microfossils of the planktonic ones are particularly useful because their skeletons can be carried by ocean currents to coat the sea bottom of an ocean.  The mixture of types can be a unique identifier of sediments that can span great distances on the ocean floor or continental rocks formed in past oceans.  Even climates of the past can be determined from isotope studies of their skeletons.

An introduction to some of the literature about bottom communities in the ocean can be found in the final few pages of the text I was working on at the time [Engemann, Joseph G., and Robert W. Hegner.  1981.  Invertebrate Zoology, 3rd ed.  Macmillan Publishing Co., New York.  746 pp.].  The references at the end of the chapter include some such as Grassle (1977, Slow recolonization of deep-sea sediment.  Nature 265:618-619); and others about sedimentation rates and other topics pertinent to the topic.

An environmental consideration

The content of the last chapter made me aware the long term effects of ocean pollution could be much more severe and persistent than localized damage to communities.  The chapter was a step along the way to understanding the extreme age potential in the abyssal region organisms.  Marine sediment communities could have a sequence of animals recolonizing them that might yield an estimate of the time of major sediment disturbances.  Such actions might blur the clarity of community lines in the fossil record.  Are we in the process of leaving a major unconformity in sediments by our actions?  The widespread dispersal of chlorinated carbon pesticides shows the potential hazard of unlimited ocean dumping of wastes, either intentionally or by contaminated rivers and atmosphere.
  
Pogonophorans

Pogonophorans living in tubes in abyssal sediments are thought to have their tubes vertically oriented in the sediments.  One line of evidence is the lack of the posterior segmented region in most dredged specimens.  Such orientation indicates they could be getting nutrition from deeper sediments that are much older; that would make carbon dating of their age a near impossibility if fossil food in the sediments is a major source of their nutrients.

The complex of ideas involved in the topic were part of the preparation enabling me to make the pogonophoran connection of protostomes and deuterostomes.  Seeing that made understanding the tree of life correctly and the error needing correction in molecular proposals of Ecdysozoa and Lophotrochozoa possible.  That eureka moment began with my reading the paper of Gans and Northcutt, 1983, as described in earlier posts on evolution and creativity.

Joseph G. Engemann     November 6, 2014 (some editing on 10/18/2015)

Friday, October 31, 2014

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

Thursday, October 23, 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

Friday, October 17, 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

Saturday, October 11, 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


Monday, October 6, 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


Saturday, October 4, 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

Wednesday, October 1, 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

Wednesday, September 17, 2014

SCIENCE

Science: Data Selection


DATA SELECTION

Scientists view data selection as forbidden.  That is certainly appropriate in a well-designed study if everything goes smoothly.  But it seems appropriate to exclude data that results from defective instrumentation, obvious errors in recording data, and inclusion of data not meant to be part of a class being compared.  Any departures from selecting data after it has been collected should be included in notes of research reports.  Even the best of intentions of researchers can sometimes result in compromised data that should never have reached publication after good peer review.  Some examples I have encountered follow.

Salamander growth 

An excellent field study done by a former colleague showed a continuously rising straight-line growth curve.  My familiarity with growth curves from investigating the principle of growth pertinent to my study of protozoans during my master's research project and crustacean growth in my doctoral research made me dubious about the salamander growth reported for the Central American salamanders.  Dr. Vial informed me that his doctoral committee had approved excluding some data thought to be defective in the study.

I was discussing his study with him after a seminar he presented about it.  Successive years data from salamanders that had not grown were excluded for fear that they were not from the same salamanders but were ones that had lost toes that made them misidentified as ones from his toe-clipped sample.  I don't remember for certain if they were also excluded for possibly not showing any growth due to tail loss and incomplete regeneration of a new tail.

It is likely that his salamanders growth slowed with age due to one or more of the many factors that can slow growth.  The rapid growth of young individuals slows and in many species stops before natural death occurs.
1. Energy put into growth diminishes as more energy is put in to reproduction.  2. Increased size may not be accompanied by an accompanying supply of materials for growth.  3. Accumulation of waste within cells may slow growth.  4.  Conversion of l-isomers of amino acids to d-isomers may interfere with metabolism.  5. Telomeres of the chromosomes may be reduced beyond numbers needed for growth.  And, 6.  Genetic control causing growth cessation may have evolved through natural selection to keep the species age class composition supplied with young and vibrant individuals.  Regions where such populations occurred would likely replace adjacent populations not doing so.

Remote sensing

Another colleague made the assumption that remote sensing of lake colors by satellite could measure lake quality.  The assumption was correct in a general way but I knew of one specific case where it did not work as planned.  Asylum Lake was one I frequently sampled with my aquatic ecology (limnology) classes.  Years of food wastes had polluted it severely although recovery was proceeding after it stopped.

During the years of his study I had noticed the surface often had many floating bits of duckweed, one of the smallest aquatic green plants.  Their chlorophyll is of a type associated with green algae that are found in lakes not severely polluted.  The algae suspended in water beneath the surface were primarily blue-green algae which are indicative of lakes over-enriched with phosphorus.  So the lake by that assessment was eutrophic and not oligotrophic as the remote sensing indicated.

Molecular biology errors

From my reference file is the following entry.
Lewin, Roger.  1988.  DNA clock conflict continues.  Science, 241:1756-1759. describes article of Charles Sibley and Jon Ahlquist using DNA hybridization criticized by Vincent Sarich and others – wrong side (Sarich) seemed to win charging selection of data but Sarich Tmode used by him is selection of a worse sort. 

Sibley's work was a study of bird relationships.  He had eliminated some data that were obviously contaminated as he knew by his experience with the technique and had properly noted in his work.  His approach seems to have been abandoned, unfortunately since it avoids data selection flaws found in much recent work.

This blog's post of 5/31/2013 entitled Science screw-up No. 1 describes a major episode still not resolved resulting in an invalid interpretation of animal phyla relationships.

Missing data

Finding data that we did not know was missing is an unforeseeable event that, when found, enabled me to see some important aspects of origin of animal groups.  Many posts starting in late June 2013 related to annelid theory of chordate origin and the pogonophorans may help clarify the significance of Webb's publications about the finding of the formerly unknown segmented posterior extremity of pogonophorans.

Estimating the time of glacial retreat in Michigan based on strata of bog vegetation carbon-dated ages has developed with a possible error.  Fossil carbon of low activity was probably incorporated in bog vegetation from carbon derived from ancient carbonate deposits dissolved in water entering lakes where the plants grew.  This missing aspect of the data would give an older age to the age estimated proportional to the percentage incorporated.

The errors and other criticized findings you may find in my blog may be indicative of the value of an old saying -  that we can or should learn from our mistakes; also that if you are afraid to make a mistake you are not likely to find anything.  I thank them all, if they hadn't tried, I wouldn't have much to say.


Joseph G. Engemann   September 17, 2014


Monday, September 15, 2014

EVOLUTION

The Error of Irreducible Complexity


FALSE SCIENTIFIC CREATIONISM ARGUMENTS

Irreducible complexity is probably the most believable of the error filled arguments of "scientific creationists."  Their attempts to credit the stories of creation found in the Bible with factual scientific truth impede others from seeing the grandeur of creation with one single creative burst giving rise to the universe and ultimately the process of evolution by which life came to exist.

Darwin's Black Box, a 1996 book by Michael Behe defines "irreducibly complex" as "a single system composed of several well-matched, interacting parts that contribute to the basic function,wherein the removal of any one of the parts causes the system to effectively cease functioning."

Darwin himself provided the argument in Chapter Six of his The Origin of Species entitled "Difficulties of the Theory".  Darwin's first sentence of a sub-section "Organs of extreme perfection and Complication" reads as follows.

"To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree."

Why the seeming absurdity may not be absurd is discussed for three pages before the sub-section concludes with the following sentence.

"Let this process go on for millions of years, and during each year on millions of individuals of many kinds; and may we not believe that a living optical instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?"

In the century and a half since Darwin presented that view, morphological and molecular evidence has accumulated that make it easier for informed biologists to understand major steps of the process.  The basic ultrastructure of the eye's retina associated with derivatives of cilia probably began with light sensitive spots on roots of cilia or flagella enabling photosynthetic flagellates to give a directional response to light when shaded by an associated pigment granule.

Most of the above is found in chapter two of my 2010 Evolution Insights manuscript which includes the following statement.

"The fact that an eye cannot function well with an essential part removed does not mean that it could not evolve gradually from one that did not have that part.  Because God did create it, either by the evolutionary process or by some more recent creative event should be answered by the facts if such exist.  Those believing in God as their creator should stop to think that God is the creator of all things either directly or by the natural processes of the one created world.  The consequence of that, a world behaving according to God's laws, is that there is truth in the correct interpretation of the evidence the world presents."

Joseph G. Engemann     September 15, 2014

Monday, August 18, 2014

CREATIVITY: Last First

The Two Way Street

Was the name of my 1974 manuscript on creativity which was never published.  Since it dealt with creativity and the value of reverse viewing, I am starting at the end with a series of cartoons it contained.


The caption "Don't say anything, he thinks he's creative." was a jab at myself.  Perhaps it was a reminder to not take myself or my ideas too seriously.  The cartoon followed the final chapter, number 13, which did not particularly talk about how to be creative, but reviewed some ideas I had entertained that did not appear in earlier chapters.

An idea for improving certification processes for teachers and my realization that administrators can be an effective source for good preceded ideas I thought important to work for as a congressman.  I did not run for congress in 1969 after thinking about it and discarding the idea.  An example of one idea entertained was the following in a section on "Social Needs."

"There were programs I was interested in pushing that were dubious campaign issues because of complexity or the potential for misunderstanding or arousing effective opposition.  As a university teacher I enjoyed a retirement program (TIAA-CREF) where my rights were immediately vested and could be taken from job to job.  Why should not all workers have that advantage?  It is especially irritating to see corporations rob older workers of their pensions by either mismanagement or corporate restructuring.  So a federally licensed pension system similar to TIAA-CREF should be a right of all."

Permission to use the above cartoon in non-profit publication or personal use is granted with the hope you will credit evolutioninsights.blogspot.com

Joseph G. Engemann    August 18, 2014