SCIENCE SCREW-UP NO. 1

The Lophotrochozoa Ecdysozoa mistake

A big mistake in the tree of life – ignoring generation time

How it started

What should be one of the crowning jewels of achievement in molecular biology has been plagued by an unwarranted suggestion in an otherwise outstanding seminal paper (Zuckerkandl and Pauling, 1965) detailing the theory of molecular clocks.  They clearly laid out the factors determining genetic changes over time.  One of the factors was generation time of organisms.  They opined that it was impossible to determine the past generation times involved in the evolution of species, but that variation in generation time factors speeding and slowing rates would average out so generation time could be ignored.  The big mistake had its basis in this presumption.

Why it should have stopped

Within a few years, Kimura and Ohta (1971) noted that the pauling (a rate of substitution of ten to the minus nine per amino acid site per year) varied from one centipauling for histones to four paulings for fibrinopeptide A.  Of course the mutation rate for the nucleotides of DNA would be somewhat higher than 400-fold because of the redundancies in the DNA coding for amino acids. 

Laird, McConaughy, and McCarthy (1969) already had reported a ten-fold higher rate of nucleotide sequence variation for rodents compared to artiodactyls when time estimates were in years and said “This difference diminishes if generations, rather than years, represent the appropriate interval of evolutionary divergence.”  Britten (1986) noted that “Examination of available measurements shows that rates of DNA change of different phylogenetic groups differ by a factor of 5.”

Miyamoto, Sllghtom, and Goodman (1987) reported “. . the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans.”  Field et al. (1988) noted that “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.”

What should have stopped

Publication and acceptance by scientists in general of the Lophotrochozoa and Ecdysozoa; papers describing the Lophotrochozoa in 1995 (Halanych et al.), the Ecdysozoa in 1997 (Aguinaldo et al.), should have been rejected by peer review.  Both studies were based on 18S ribosomal DNA sequences.  Both run counter to results of classical phylogeny studies preceding molecular phylogenies; then the establishment accepts the contrary results of these two small samples although the authors noted several things that should have raised questions. 

For the 1995 Lophotrochozoa study, note 10 includes the following statement “Regions that could not be readily aligned were excluded from the analyses.”  And the 1997 Ecdysozoa paper says “It was unexpected to find nematodes contained within the Ecdysozoa because in previous molecular studies they diverged deep in the protostome tree, even before the deuterostome-protostome bifurcation.”  It seems that both reports were state of the art for molecular phylogeny studies of smaller evolutionary units having less variation in basic life cycles and molecular features.  So the problem is one of scale; errors are compounded when generation time is ignored.  The fact that small scale projections are not greatly affected must have made the authors and their peers think the new broad-scale studies were correct.  Big mistake.

It has been said that hindsight is 20/20

Sanderson (1996) would have shown them their sample size was too small.  Other alerts are now available from Maley and Marshall (1998), Martin and Palumbi (1993), Wägele (1999), and many others.  But with no correction for generation time in their algorithms, it was GIGO.  Computers can generate trees regardless of the quality of the input.  Unfortunately, the flawed results have been accepted and perpetuated in textbooks and additional research.

Disclaimer for conflict of interest

I admit to a certain amount of pique with both Nature and Science for having rejected manuscripts I submitted years ago that might have had a role in providing a better solution to the evolutionary tree of life.   I understand the need to reject over 90% of submissions means life is not necessarily fair for those seeking publication.  I made a 1988 presentation to the Michigan Academy entitled “A life cycle adjustment is needed for molecular clocks”.  In 2004 I presented “Ecdysozoa, Lophotrochozoa, and Other Molecular Phylogeny, Peer-Review Failures. “  The abstract was in the Michigan Academician, 36(1):118-119. I intended to submit the full paper to Science, but found their new submission rules beyond my digital capabilities.  More about the answers I have for evolutionary questions will be presented in future postings.   I might have accepted the Lophotrochozoa and Ecdysozoa proposal if I did not already have knowledge of a tree of life that better fits the facts; the pogonophorans provide critical information supporting the tree.

Joseph G. Engemann, Emeritus Professor of Biological Science, Western Michigan University,  Kalamazoo, MI   May 31, 2013

References cited

Aguinaldo, Anna Marie A., James M. Turbeville, Lawrence S. Linford, Maria C. Rivera, James R. Garey, Rudolf A. Raff, and James A. Lake.  1997.  Evidence for a clade of nematodes, arthropods and other moulting animals.  Nature, 387:489-493.

Britten, Roy J.  1986.  Rates of DNA sequence evolution differ between taxonomic groups.  Science, 231:1393-1398.  

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.

Halanych, Kenneth M., John D. Bacheller, Anna Marie A. Aguinaldo, Stephanie M. Liva, David M. Hillis, and James A. Lake.  1995.  Evidence from 18S ribosomal DNA that the lophophorates are protostome animals.  Science, 267:1641-1643. 

Kimura, Motoo, and Tomoko Ohta.  1971. On the rate of molecular evolution.  J. Molec. Evolution, 1:1-17.

Laird, Charles D., Betty L. McConaughy, and Brian J. McCarthy.  1969.  Rate of fixation of nucleotide substitutions in evolution.  Nature, 224:149-154.

Maley, Laura E., and Charles R. Marshall.  1998.  The coming of age of molecular systematics.  Science, 279:505-506. 

Martin, Andrew P., and Stephen R. Palumbi.  1993.  Body size, metabolic rate, generation time, and the molecular clock.  Proc. Natl. Acad. Sci. USA, 90:4087-4091.

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.

Sanderson, Michael J.  1996.  How many taxa must be sampled to identify the root node of a large clade?  Syst. Biol., 45:168-173. 

Wägele, Johann-Wolfgang.  1999.  Major sources of errors in phylogenetic systematics.  Zool. Anz., 283:329-337. 

Zuckerkandl, Emile, and Linus Pauling.  1965.  Evolutionary divergence and convergence in proteins.  Pp. 97-166.  In: V. Bryson and H. J. Vogel (eds.).  Evolving Genes and Proteins.  Academic Press, N. Y.

GOD

God

    infinite    pure spirit    caring    personal     creative creator

This posting should be first in order of importance and causality.  I think God has been intimately involved in my life, enabling me to see details of how he created the living world through the process of evolution.  But I cannot prove that to the satisfaction of those uncertain about God’s existence.  Nor do I rely on that belief to come to my conclusions about evolution, creativity, or science.

Old and New Testament scriptures have much to say about God being the creator, from the Genesis accounts to the epistles of St. Paul.  But the details told in stories lacking the foundations of modern science should not detract from the ultimate message of God’s awesome role in creation.

Over two thousand years ago Aristotle provided four proofs for the existence of God.  I think they are all derived from the principle of causality upon which all scientists rely.  But the transition from pure existence, the “I AM” revealed millennia ago, to the material world is beyond the understanding of many.  The hurting and evil in the world impede many from seeing the goodness and greatness of God.  A full understanding of evolution and free will is helpful in getting past those impediments.  More may eventually be said about that topic.

As a graduate student I became a close friend of a young faculty member in zoology and was an occasional guest in his home with his family.  He maintained I would be handicapped as a scientist because the dogmatic thinking associated with my religion would interfere with my thought processes.  I don’t remember if I had an appropriate response, but in the 56 years since then I do see what makes his conclusion wrong.  You don’t have to believe in God to be a “dogmatic thinker”.  And a firm belief in causality will help you look for answers when doubters lose heart.

I have been helped in my spiritual journey by association with people from many lands, of different religions, and varying views and backgrounds.  I can see the good in all of them, the flaws we share, and almost understand God’s love for all of them; I do so thankfully, perhaps motivated by the thought that then there is hope for me.

I may eventually post a few pictures of houses of worship around the world.  But great inspiration can be had in contemplating a stand of mature trees, the night sky, the waves lapping the ocean shore, the view from mountaintops, the Grand Canyon, Niagara Falls, and the myriad life forms in a drop of pond water on a microscope slide.  But to really know the creator, we should look for God's reflection in people.

Written 4/2/2011, slightly edited and posted 5/21/2013        Joseph G. Engemann

CREATIVITY and COGNITIVE DISSONANCE

Creativity and Cognitive Dissonance

COGNITIVE DISSONANCE, the protostome-deuterostome missing link found

The insoluble clash of mutually exclusive ideas may trigger creative solutions.  This post was not edited from a previously written project as I intended to do for posts.  So it is subject to being posted with lack of checking on details.  But the term cognitive dissonance was one I learned of a long time ago in a workshop on teaching provided colleagues at Western Michigan University by Dr. Robert Travers and Dr. Greg Fisk.  They were emphasizing creative approaches to teaching.

The previous post on creativity was one I was pleasantly surprised at getting posted since I had been having problems doing so.  The morning paper inspired me.  In it were two columns using the term cognitive dissonance; a term I have only found in the newspaper a few times before.  One, on the first page of The Wall Street Journal Sunday inclusion within the business section written by Brett Arends (WSJ.com/Sunday), even used a cartoon illustration to show stock prices and interest rates make the bull and bear riders an instance of being on the same financial roller coaster, hence a case of cognitive dissonance.  Stock prices and interest rates typically go in opposite directions.

My most enlightening case of cognitive dissonance was finding a worm that was put in two disparate parts of the animal kingdom.  The conventional view put them in the annelid line of animals.  A new view (Gans and Northcutt, 1983) put them in the opposite cluster of animals that humans are in based on their common embryology.  I knew the existing data meant they had to be annelids, the new study noted they were in the vertebrate line based on embryology.  I was somewhat irritated and distressed by what I knew, the new study had to be wrong.

As I thought how honest scientists have to be and how careful they are with their data I somehow thought the only way it could be true would be if the worms were an intermediate connecting link.  The eureka moment came almost instantly, blending knowledge of the old annelid theory that had been rejected with the new embryological similarity to the vertebrate line.  Differences were so great it had previously been thought to be necessary to go back to the flatworms to have a likely common ancestor for the annelid line and the vertebrate line.

The many other bits of evidence for the vertebrate line originating from the annelid level of animal development rapidly became apparent thanks to merger of disparate facts gained from others and from my research.

Gans, Carl, and R. Glenn Northcutt.  1983.  Neural crest and the origin of vertebrates: a new head.  Science, 220:268-274.  (15 April 1983)  Includes Pogonophora in the deuterostomes.  “. . .  the neural crest and the epidermal placodes for special sense organs and other neural structures.  These structures may be homologous to portions of the epidermal nerve plexus of protochordates.  The transition to vertebrates apparently was associated with a shift from a passive to an active mode of predation, so that many of the features occurring only in vertebrates became concentrated in the head.”  This article triggered my (1983 eureka event) awareness of the pogonophorans as the protostome-deuterostome link after initial disgust at their inclusion in the deuterostomes.

           Joseph G. Engemann   May 19, 2013 

CREATIVITY

CREATIVITY

My unpublished 1974 manuscript, The Two Way Street, was subtitled One Approach to Creativity.  It was prompted by my observation that the evolutionary sequences or ancestral trees of groups of related organisms constructed by different scientists were sometimes reversed from those of others.  Sequencing the gradual changes in an evolutionary lineage does not tell which end of the sequence was the starting point.  The fossil record or other data may help in that determination.  But increasing size and increasing complexity cannot be assumed to be pointing to the newer species.

I thought I might be creative because I had two patent searches done for two different product ideas. The Two Way Street was my attempt to describe principles of creativity.  I did not research the subject because I was familiar with a maxim of Nikko Tinbergen noting that novices are more likely to make creative discoveries than those well versed in the principles of something.  It seems the learned know all the things that lead to the state of the art knowledge and cannot escape the rut that brings them to exactly where they already are.  The novice can make breakthroughs by trying things the experts already know will not work.  Surprise, the newcomer makes the remarkable breakthrough.

After writing The Two Way Street I went to the creativity literature.  I thought my idea that humor would be an important contributor to formation of a creative person was original.  But Koestler’s remarkable book on creativity treated humor extensively.  Others had treated my main theme of looking at things from another point view as well, some called it reverse viewing.  I had systematized mental manipulations as ways of thinking about something to get different, and possibly useful, new views.  I may eventually blog about each one, but the manuscript outlined the types of manipulations useful in handling facts and ideas for development of creative solutions.

Manipulations can be categorized as combinations, deletions, substitutions, permutations, extensions, or models.  Permutations can be subdivided into ones that are angular or sequenced ones.  Angular ones can be inversions, reversals, or rotations.  Sequencing can be done according to time, size, complexity, development, or the parameter of your choice.

Biological phenomena were uppermost in my mind when constructing the list.  But my first possible useful patent search had been for a combination.  I had wanted to be an inventor.  The lead pencil with the attached eraser impressed me with the value of combinations.  So I found that my idea of making a hunting knife with a hollow handle that could be used as a match safe or for storage of other items of use to a camper answered my musings.  The closest patent was for a jackknife with two compartments making up the sides of the handle.  I never got to discuss my idea with a knife manufacturer, but the fall-out was the first on the list above of mental manipulations useful for solitary brain-storming.

Models can be mathematical, conceptual, or spatial.  Evolution and natural selection have been used as models for social and economic phenomena.

Joseph G. Engemann

EVOLUTION

Evolution and Asteroid Strikes

ASTEROID STRIKES HELPED SHAPE OUR EVOLUTION

Where would we be without asteroid strikes? 
                                   

We might still be here, but we would look entirely different.  Bombardment with asteroids and other space debris was much more common a billion years ago.  At that time life in our ancestral line had reached a worm-like stage that also gave rise to some other forms less like our egocentric selves.  The bombardment had an enormous impact on the course of evolution.

When God created the universe it began as a speck over twelve billion years ago as we measure time.  That speck was endowed with the properties that would spawn several generations of stars and the galaxies we see today.  It had all the potential for the formation of elements and star systems with associated planets as well as the evolution of life as we know it.  Darwin realized this as the work of the Creator before events sped his drift into agnosticism.

I know, from the things science has discovered, some major things that answer a few major evolutionary questions.  It is not because of personal brilliance or planning that I know them.  It is not because of some revelation that I know them.  It is the result of an unusual set of circumstances which I, have blundered into and, now view as God’s direction of the chance events that made it possible for me to put the bits of the puzzle together.

In 1987 two paleontologists (Raup and Sepkoski) published a study of extinction rates that showed high peaks associated with major asteroid impacts.  A regression line, which I calculated from their data, projected back over half a billion years to the beginning of the Cambrian where it reached a 100% extinction rate.  That obviously did not occur because there are Pre-Cambrian fossils, some of which had remains looking much like tubes of pogonophorans, which still live in the abyssal regions of the ocean bottom.

Pogonophorans were able to survive the Precambrian bombardment because they had evolved by natural selection to survive by absorbing nutrients from sediment and lost many of the typical annelid worm features of their ancestors.  They even lost the mouth and rigid early embryological features of their ancestral annelids.  Some changes now evident in their descendants led to, among other things- our systems being upside down as compared to most worms, our fertilized egg’s ability to have each of the early cells survive as twins or multiple births instead of dying when separated, and our pituitary to have its peculiar blend of hormones (the endodermal and ectodermal tissues that form the pituitary couldn't have joined if the pogonophoran pharyngeal region had not been suppressed during the period the former circumesophageal nerves were fusing).

Biologists think ancestral forms are replaced by new forms and cannot be found unchanged today.  But pogonophorans, because of the peculiar features of the deep sea have extremely long lives as individuals and thus those that stayed there evolved very slowly.

Many astronomers have come to believe the moon (Wikipedia, moon formation) started as a result of a collision of the earth with another heavenly body.  They believe the probability is very minuscule, but why bother when it is obvious that the following is much more likely.  The asteroid belt consists of orbiting fragments from a collision of two or more planets, or a planet and another major object, in that region between the orbits of Mars and Jupiter.  The scars on the moon, other planets, and large asteroids show the evidence of past impacts.  This immense accumulation of space debris was sufficient to slow the moon’s rotation so gravity’s effect could bring it to zero rotation with respect to the earth.  The earth’s greater mass was sufficient to keep it rotating even though we probably received more mass from space than did the moon, slowing us from 400 plus rotations per year to 365.  Tidal friction is used to explain the slowing of rotation for both the moon and the earth; but, shouldn't it have been more dramatically slowed for the earth with its oceans if that were true?

So we have cleaned out most of the fragments in earth’s orbital path and have a much reduced probability of an earth shattering strike from outer space than in prehistoric times.  The relative peace with the reduction or cessation of celestial bombardment, the last really major event being the strike that helped end the dinosaurs at the end of the Mesozoic about sixty-five million years ago, left a partial void that was repopulated in part by survivors from the deep sea.  The process of re-population from the deep-sea was much more important as the Cambrian began.

Incidentally, the idea of annelid worms being in our ancestral line was much more popular a hundred years ago.  Our annelid ancestry was rejected because of the great differences in embryology of annelids as compared to the vertebrates and invertebrates sharing our ancestral line starting with the pogonophorans.  When genetic information helped us see that the embryological differences were not the complete answer, the old annelid origin theory was not restored.  DNA/RNA studies are excellent for determining the relationships of closely related organisms.  Nucleic acid studies, as currently performed, have not yet been refined enough to project distant relationships. We know more about distant relationships from other data for widely different groups.

Almost anybody can write a book.  I've written a manuscript for one explaining some of the above.  But it runs counter to popular opinion of most students of evolution.  Why?  Probably because few biologists today have time for the range of course work common in my generation.  I had to dig into the literature on pogonophorans to revise an invertebrate zoology text for a second edition that was published in 1968.  I found that they must live for several thousand or more years, thanks, in part, to my knowledge of marine biology.  I might not have realized that if I hadn't developed an interest in causes of longevity during my doctoral studies (at MSU) comparing Michigan and Tasmanian isopod crustaceans (thanks to a 1956 Fulbright Grant for study at the University of Tasmania).

So the obscure pogonophorans that weren't even known about a hundred years ago provide important clues.  They show up in odd places in molecular studies of evolution because they have changed only slightly genetically while more recent groups have changed greatly.  Thus the great differences between the extremes of more recent groups are greater than the difference between either of the extremes and the pogonophorans.  I know it is due to the ancestral position of the pogonophorans and their extreme length of life.  My evolutionary colleagues think it can be explained away as an anomaly called “long-branch attraction”.

If my argument that major asteroid strikes are remarkably less likely in the future than in the past does not comfort you, consider the following.  If strikes are random, the likelihood of a strike is directly proportional to the area considered.  The mid-February one exploded above Chelyabinsk, Russia. On average, for every 63 that hit Russia, the largest country in the world, only 36 would hit the United States; about 100 would hit Russia while 1 is hitting Michigan; Liechtenstein would get about one strike for every 100,000 to hit Russia.  Kalamazoo is smaller than Liechtenstein, so sleep well tonight.  If you are still worried, remember that the one hitting Russia is only about the second big one to hit in the past one hundred and five years, the other knocked down trees over a large area in Siberia.

Oh, by the way, the regression line that I calculated hit 100% extinction rate at the beginning of the Cambrian, if I remember correctly, projecting forward, it did not hit zero anytime soon.  But with strikes in our area likely to be about once every twenty million years there doesn't seem to be much to worry about if the injuries are no worse than in Chelyabinsk.

Joseph G. Engemann, Kalamazoo, Michigan, Emeritus Professor of Biological Science, Western Michigan University. 

This was written for, but not sent, to the Kalamazoo Gazette letters editor in late February. Edited 5/11/13.

My Evolution Blog

Evolution, science, creativity, and God are among many ideas I would like to share with you.  They come from sixty or more years thinking about science, evolution, creativity, and God.  Some are new and not yet incorporated in the body of science common to those in my field.  For example, a worm that lives for thousands of years provides evidence of the connection of vertebrates to annelid ancestors.

Some important ideas come from my Fulbright research at the University of Tasmania followed by research at Michigan State University.  Crustaceans with greatly different life-cycles made me very alert to factors influencing longevity.  The Tasmanian ones were in pools on Mount Wellington that Darwin had passed over a century before me when he climbed the mountain as noted in his Voyage of the Beagle.  Then I became aware of the ancient worms when I revised an invertebrate zoology text for the second edition (Hegner and Engemann, 1968).  They had not been included in the first edition when I had used it as a student in about 1947.  Others thought they were an aberrant dead-end from an evolutionary standpoint.  But they help answer many important evolutionary questions.

Seeing why others don't know about it led me to understand some of the problems with peer review, scientific journals,and scientific thinking.  Along the way I wrote an unpublished manuscript on creativity.  I also note the creation/evolution debate does not need to be a conflict.  Those who believe in God should realize the creator can make us through or along with the process of natural selection and evolution.

My computer exposure has gone from punch cards in the 1960's through a succession of upgrades.  It has bogged down in recent years with the advent of programs that do most anything you want - if you know how to use the software.  But I can't even figure out how to get to editing portion of this to put my biography in it. Maybe I will eventually get to it.  When I do you will know it because pictures and illustrations will help to make some of things I want to say understandable.  Seventeen years of retirement after 36 years of teaching invertebrate zoology and related subjects at Western Michigan University helped me compile some of the things I want to present.  I've decided to do it now because my children and grandchildren are busy enough that they are unlikely to do it for me posthumously.

Today, December 23, 2014, over one year and seven months after the above was posted (5/19/13), I was trying to set up a new blog to transfer items on God and Creativity to, as well as to accept new items on those two as well as favorite pictures and comments not related to evolution.  As I went through the areas I had hoped to use to accomplish that I was unable to get Blogger or blogspot.com's attention for that purpose.  But I did find out my name is Evolution Insights instead of Joseph G. Engemann or my preferred Joe Engemann. My initial thought about a week ago was that I really needed to set up four or more blogs to allow readers to access their area of interest with greater ease.  To some extent, it can already be done by clicking on the topics at the top of the blog.

Joe Engemann (my name, missing in the original 5/19/13 post 1)  Kalamazoo. MI   12/23/2014