Sunday, June 30, 2013


EVOLUTION – ANNELID THEORY BIBLIOGRAPHY a supplement to earlier post today.  

I will not feel bad if you don’t read this, even if you are a biologist.  If you have a specific interest in annelid theory of chordate origin, the references may be helpful.

The references below are some that I found useful in understanding the evolution of the animal phyla, especially as pertains to the annelid theory.  They tend to focus on molecular aspects if I thought they shed light on the problem.  The bibliography is a partial one and could have been greatly expanded if for example, I included all those that did not make a link to both protostomes and deuterostomes [Akam, Michael, 1998, Biol. Bull., 195:373-374 deals with shifts in Hox gene expression in segments during evolution of arthropods] or my database was defective [a 1978 invertebrate collagens article in Science, 202:591-598 has an obvious defect in the author’s name(s)].  Since disappointment with the defects [noted in my 5/31/13 post] of some phylogenetic studies over a decade ago, I have not been very attentive to subsequent reports.

Arendt, D., and K. Nübler-Jung.  1994.  Inversion of dorsoventral axis?  Nature, 371:26. 

Arendt, Detlev, Ulrich Technau, and Joachim Wittbrodt.  2001.  Evolution of the bilaterian larval foregut.  Nature, 409:81-85.

De Robertis, E. M., and Yoshiki Sasai.  1996.  A common plan for dorsoventral patterning in Bilateria.  Nature, 380:37-40.

Eakin, Richard M. 1979.  Evolutionary significance of photoreceptors: in retrospect.  Am. Zool., 19:647-653.    Fig. 1 shows great similarity of photoreceptors of annelids and cephalochordates although he puts them near the tips of separate lines

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.”

Gardiner, Stephen L., and Meredith L. Jones.  1985.  Ultrastructure of spermiogenesis in the vestimentiferans tube worm Riftia pachyptila (Pogonophora: Obturata).  Trans. Am. Microsc. Soc., 104(1):19-44.

Gould, James L.  1985.  How bees remember flower shapes.  Science, 227:1492-1494.  “presumptive vertebrate-invertebrate dichotomy is false”  bees use search and memory process similar to vertebrates.

Lull, Richard Swann.  1945.  Organic Evolution.  Macmillan, New York.  744pp. [Revised edition, 1929, earlier 1917] a paleontologist at Yale.  Fig. 123, page 429 after Wilder of annelid theory of vertebrate origin

Meurling, Patrick.  1967.  The vascularization of the pituitary in elasmobranchs.  Sarsia, 28:1-104. 

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.” 

Moore, Richard C., and Michael D. Purugganan.  2003.  The early stages of duplicate gene evolution.  Proc. Natl. Acad. Sci. USA, 100:15682-15687.  “Gene duplications are one of the primary driving forces in the evolution of genomes and genetic systems.”

Pellettieri, Jason, and Geraldine Seydoux.  2002.  Anterior-posterior polarity in C. elegans and Drosophia-PARallels and differences.  Science, 298:1946-1950. “par” genes important in polarization for C. elegans embryo; homologs were discovered in mammals, this study looks at fruit fly

Peterson, Kevin J., Steven Q. Irvine, R. Andrew Cameron, and Eric H. Davidson.  2000.  Quantitative assessment of Hox complex expression in the indirect development of the polychaete annelid Chaetopterus sp.  Proc. Natl. Acad. Sci. USA, 97:4487-4492.  they found a similar Hox complex utilization in cells for adult body plan in the polychaete to that process described in the sea urchin

Ritzmann, Roy E., Martha L. Tobias, and Charles R. Fourtner.  1980.  Flight activity initiated via giant interneurons of the cockroach: evidence for bifunctional trigger interneurons.  Science, 210:443-445.  “command or trigger interneurons have been identified . . . .  including annelids, arthropod, mollusks, and turtle (1).” 

Romer, Alfred Sherwood.  1962.  The Vertebrate Body, 3rd edition.  Saunders, Philadelphia.  627 pp.    Illustration of annelid theory of chordate origin is on page 25 (same as Lull one but different caption) see pages 298-299 for transition in position of structures leading to pituitary – p. 298

Ruppert, Edward E., and Elizabeth J. Balser.  1986.  Nephridia in the larvae of hemichordates and echinoderms.  Biol. Bull., 171:188-196. 

Sarnat, Harvey B.  1984.  Muscle histochemistry of the planarian Dugesia tigrina (Turbellaria: Tricladida): implications in the evolution of muscle.  Trans. Am. Microsc. Soc., 103(3):284-294. 

Schwenk, Kurt, and Günter P. Wagner.  2001.  Function and the evolution of phenotypic stability: connecting  pattern to process.  Amer. Zool., 41:552-563. 

Smith, Peter R., Edward E. Ruppert, and Stephen L. Gardiner.  1987.  A deuterostome-like nephridium in the mitraria larva of Owenia fusiformis (Polychaeta, Annelida).  Biol. Bull., 172:315-323.

Southward, Alan J., and Eve C. Southward.  1982.  The role of dissolved organic matter in the nutrition of deep-sea benthos.  Amer. Zool., 22:647-658.  

Stein, Elizabeth A., and Edwin L. Cooper.  1983.  Inflammatory responses in annelids.  Am. Zool., 23:145-156.  inflammation of vertebrates and annelids shows related factors – histamine, agglutinins, lysins, etc.  also have amoeboid phagocytic cells   

Stoichet, Sarah A., Talat H. Malik, Joel H. Rothman, and Ramesh A. Shivdasani.  2000.  Action of the Caenorhabditis elegans GATA factor END-1 in Xenopus suggests that similar mechanisms initiate endoderm development in ecdysozoa and vertebrates.  Proc. Nat. Acad. Sci., USA, 97:4076-4081.

Terwilliger, R. C., and N. B. Terwilliger.  1987.  Are pogonophoran and annelid extracellular hemoglobin structures similar to one another?  Am. Zoologist, 27(4):32A, abstract #152.  Yes for Vestimentifera which also have a smaller Hb similar to one found in Perivata 

Tiplady, Brian, and Morris Goodman.  1977.  Primitive haemoglobin.  J. Mol. Evol., 9:343-347.  “The variations in nucleotide substitution rates were interpreted in terms of Darwinian selection, the emergence of a new function being followed by a rapid rate of evolution, which then slows down once the molecule has been optimized.” 

Tomarov, Stanislav I., Patrick Callaerts, Lidia Kos, Rina Zinovieva, Georg Halder, Walter Gehring, and Joram Piatigorsky.  1997.  Squid Pax-6 and eye development.  Proc. Natl. Acad. Sci. USA, 94:2421-2426. (March 1997)  Pax-6 in vertebrates and its homolog eyeless in Drosophila are known to be essential for eye development.”

Wagner, Gunte P., Chris Amemiya, and Frank Ruddle.  2003.  Hox cluster duplications and the opportunity for evolutionary novelties.  Proc. Natl. Acad. Sci. USA, 100:14603-14606.  “Hox genes play a key role in animal body plan development.  These genes tend to occur in tightly linked clusters in the genome.  Vertebrates and invertebrates differ in their Hox cluster number, with vertebrates having multiple clusters and invertebrates usually having only one.”

Joseph G. Engemann    June 30, 2013



Segmentation as a starting point

Annelids are the animals most like the ancestral form of all coelomates.  Their segmentation enabled the speedy evolution of diversity.  That diversity includes forms that show little evidence of the remnants of segmentation.  Metamerism, of chordates and some other phyla, is the repetition of organs or structure along the length of a body that no longer has segmentation.

The serial repetition of structures enables regional modification of appendages and other structures from a relatively complex base with minimal genetic changes.  This is illustrated most clearly by arthropod appendages.  It is evident in our own pectoral and pelvic appendages, although not so obviously having an early stage of origin in segmentation.  Our early embryo has some of the more convincing evidence in myotomes; adults have vertebrae with paired nerves, blood vessels, and muscles that may also be convincing.

Reduction of segmentation in the chordate line was a result of its loss by pogonophorans in the portion of the body retained in hemichordate evolution.  Most mollusks lost evidence of metamerism as a result of the shell removing benefits of obvious metamerism. A vermiform fossil shows evidence of the annelid origin of mollusks (Sutton et al. 2001); and a fossil, Neopilina, shows a more molluscan intermediate stage (Lemche, 1957).   Arthropods have striking evidence of metamerism externally in most groups, both with skeletal segmentation and appendages
Just as segmentation was modified beyond easy recognition, the coelom was also greatly modified as higher animals diversified.  Coeloms, found in both the protostome line and the deuterostome line, but not in animals earlier than annelids, provide evidence of the annelid origin of coelomates.


Water and salt regulation is an important function of our kidney.  The annelid nephridium, with pairs in most of their segments, was modified by evolution into the nephrons of our kidneys; an intermediate connection is shown by Ruppert and Balser, 1986.  The oviduct also seems to be a nephron modification.  The water-vascular system of echinoderms may be derived from nephridia; the water-vascular system stays open to the exterior, indicating the echinoderms have probably lost the benefits of osmoregulation and thus never were able to survive in fresh water.


The central position of annelids in the ancestry of coelomates may be illustrated by blood pigments.  Polychaete worms have as many as four different oxygen transporting pigments in the blood.  Higher forms typically have one of those pigments, in our case, hemoglobin.

Other Molecular Evidence

Once I thought the Pogonophora were the deuterostome connection to protostomes (1983), I found a lot of supporting molecular evidence.  One of the first was the finding of Lipman and Pearson (1985) that crayfish Trypsin I is high-scoring for similarity to bovine trypsinogen.

The interpretation of molecular evidence is complicated by the fact that vertebrates tend to have some important genetic features in family clusters of genes whereas other animals typically have only one from a family.  Also, the same molecules may act in somewhat similar but different ways in different groups.  Hobmayer et al. (2000) found the WNT signaling pathway that had been found in nematodes, insects, and vertebrates (all with bilateral symmetry) also acted in axis formation of a radially symmetric cnidarian.

The protostome-deuterostome transition via pogonophorans may be returned to at some later date.  I expect to end the topic with my next post of a few additional references, some annotated, from my reference file that deal in some way with the topic, most about molecular evidence.

In summary, a wide variety of evidence points to the basic truth of the annelid theory of chordate origin.

   Hobmayer, Bert, Fabian Rentzsch, and 6 others.  2000.  WNT signaling molecules act in axis formation in the diploblastic metazoan HydraNature, 407:186-189.
   Lemche, H.  1957.  A new living deep-sea mollusk of the Cambro-Devonian class Monoplacophora.  Nature, 179:413-416.
   Lipman, David J., and William R. Pearson.  1985.  Rapid and sensitive protein similarity searches.  Science, 227:1435-1441.
   Ruppert, Edward E., and Elizabeth J. Balser.  1986.  Nephridia in the larvae of hemichordates and echinoderms.  Biol. Bull., 171:188-196.
   Sutton, Mark D., Derek E. G. Briggs, David J. Siveter and Derek J. Siveter.  2001.  An exceptionally preserved vermiform mollusc from the Silurian of England.  Nature, 410:461-463.

Joseph G. Engemann    June 30, 2013

Friday, June 28, 2013

EVOLUTION of systems inversion


Several major steps were involved in the inversion of systems as polychaete annelids gave rise to the chordate line of deuterostomes. 

First a branch of tube-dwelling, bottom-dwelling polychaetes evolved with some reduction of clear segmentation; development of a plume of tentacles for feeding and/or respiration probably was occurring as well.  A variety of marine species having a similar intermediate condition still exist.

The second major step involved the complete adaptation to life in abyssal sediments as pogonophoran worms.  This included (1) a loss of dorso-ventral distinctions common to species ancestral to groups with radial symmetry, (2) reduction of development of the gut, (3) increased reliance on passive absorption of nutrients, and (3) retention of the circulatory system to provide oxygen to the portion of the worm embedded in low oxygen sediments. 

The embryological changes noted in the previous post were occurring simultaneously with these changes.  They now are the pogonophorans, well-adapted to survive the extinction events of pre-Cambrian times.  The major feature identifying them as annelid descendants was the extreme lower segmented and setae bearing portion that was not noticed in specimens of early collections made by dredges that did not retrieve whole worms; the deeply embedded part presumably was left in the ocean bottom.

The third major step in the protostome-deuterostome journey was the sequence of changes as descendants moved to shallower seas during the period following the intense asteroid bombardment (see May 11 post).  Those moving from their tubes to reach particulate food more abundant on shallower sea sediments found it less jarring to the nervous system to emerge with the previous ventral nervous system of the annelids positioned so it was nearer the upper surface.  In such a position, a remnant of the gut, perhaps more substantial because of the greater abundance of food, put endodermal and ectodermal tissue closer together to induce the mouth formation associated with such an event.

A further consequence of this new position of the mouth enabled fusion of ganglia and connectives to form a brain without encircling the esophagus.  These and other changes above were facilitated by natural selection of those with genetic modifications better serving the processes.

The culmination of this process needed very little fine tuning to make a hemichordate, probably the closest annelid derivative to the chordate line of deuterostomes.  The larval stages of pogonophorans and hemichordates are very similar.  Correspondence of the anterior of a hemichordate and the upper portion of a certain pogonophorans is quite similar.  The lowest segmented portion of the pogonophoran degenerated to leave three body regions some think are characteristic of chordates.  Previous discussions indicated the speed of loss of features not contributing to survival by the greater energy left over for reproduction is a common feature in evolutionary events.

Clearly, pogonophorans are excellent candidates for the missing link clarifying the inversion of systems suggested by the annelid theory of chordate origin.  


Joseph G. Engemann    June 28, 2013

Monday, June 24, 2013



Annelid theory as a working hypothesis

Since Gans and Northcutt (1983) provided evidence of a close relative of annelids having some features of development resembling deuterostomes, as noted in the previous post, it is reasonable to evaluate other evidence.  Inversion of systems, the primary evidence supporting the annelid theory, has been deemed inadequate by those who comment.  But much other evidence is available.  The biggest impediment had been the drastic embryological differences between protostomes and deuterostomes.

Embryological evidence

My doctoral thesis research included a comparison of development of two species of isopods with very different life cycle rates of development as well as a new embryological structure in one species.  The rapidly developing egg of the Michigan species was smaller, had a thinner egg shell, and two appendages on the egg.  The Tasmanian one had a thicker egg shell and no appendage; but on the each side of the embryo within the egg was a yolk filled bulge in the position from which the other ones had their egg appendages develop.

Otherwise, both embryos packed the egg fully.  They both developed in a folded position, legs outermost.  But the flattening differs so the Tasmanian one filled up space with the yolk filled bulge.  The Tasmanian species has less change from ancestral crustacean features; they also lack the abundant source of food from deciduous tree leaves as available for the Michigan ones.

The main point of this isopod egg observation is that the evolution of a new feature in the egg goes counter to what many biologists think was perhaps a valid portion of the discredited “biogenetic law”.  The law is not absolute, especially as my observation showed me, evolution can occur by the development of new features in the earliest life stages of an organism.  Clearly, embryological stages do not faithfully repeat steps in the evolution of the organism. 

Since the pogonophorans are likely candidates as intermediates, in spite of the general opinion that they were an evolutionary dead-end, what do they contribute to the story?  Well, they have lost the annelid digestive system in the adult, their segmentation has nearly disappeared, and they live in an abyssal world with a very low rate of input of food.  Such a regime would drastically select options or mutations that save energy. 

Why protostome spiral cleavage became deuterostome radial cleavage

The thinning of the egg shell would not constrain the early dividing cells into the packed spiral pattern of ancestral protostomes but it would conserve resources otherwise used for a strong egg shell.  Consequently, the loss of structural integrity of the egg shell would not impose the constraints for efficient use of space as in spiral cleavage.

Limited energy and resulting low reproductive potential puts survival at a premium for the individual.  Thus, although the first cell divisions (cleavage) of protostome eggs end the potential of the daughter cells to each develop into individuals, it is possible for each of the early dividing cells of the deuterostome egg.  Injury or death of one of the first few cells of a deuterostome egg would not necessarily result in death.  In fact, identical twins, triplets, and other genetically identical individuals could not have developed if deuterostomes had retained the features of spiral cleavage.  The survival advantage of this feature for pogonophoran species in the nutrient poor abyss should be an obvious benefit.

In both cases it is a loss, loss or reduced production of shell, loss of control of early developmental specification.  As discussed in an earlier post, loss can occur more rapidly than gain of a feature.  The rates are relative to other factors such as food supply, generation time, and value of the features for survival.  But clearly, pogonophorans are excellent candidates for the missing link connecting embryological features of protostomes and deuterostomes.  The conclusion is hypothetical.  The event described was undoubtedly a Pre-Cambrian occurrence.  But the conclusion is based on comparative evidence consistent with similar conclusions that will be presented for other evidence.

Interesting, but somewhat irrelevant to the current discussion is the fact that the Michigan isopod egg appendage had the cellular appearance of adult respiratory tissue and must aide their relatively rapid development.


Engemann, Joseph G.  1963.  A Comparison of the Anatomy and Natural History of Colubotelson thomsoni Nicholls, a South Temperate, Fresh-water Isopod and Asellus communis Say, a North Temperate, Fresh-water Isopod.  Ph.D. Thesis, Michigan State University, East Lansing.  146 pp.

Gans, Carl, and R. Glenn Northcutt.  1983.  Neural crest and the origin of vertebrates: a new head.  Science, 220:268-274.


A United States Fulbright Grant for study in Australia, aide of staff and use of facilities at the University of Tasmania and Michigan State University, as well as a Faculty Research Grant at Western Michigan University, were instrumental in my making many observations involved in this series of blogs.  Many individuals deserve my thanks as well.

Joseph G. Engemann     June 24, 2013

Sunday, June 23, 2013



Abandoned views

Once natural selection was accepted as the way evolution of species produced the variety of life on earth, it became a goal to determine the ancestral line of intermediate forms leading to the major groups of animals.  A series of successive creations suggested by the drastic changes in the geologic fossil record had earlier been suggested but abandoned.  Likewise the concept of inheritance of acquired characteristics was seldom considered after an understanding of genetic inheritance developed.

Features of some value

Radial symmetry versus bilateral symmetry was given some emphasis for a while.  The grades of body complexity were, and still are, given considerable significance.  Grades went from cellular level, to tissue level, to organ system level.  The most primitive of those with organ systems had only a mouth opening, whereas the more advanced had both mouth and anus.  Blood vascular systems represented a greater advance.  Skeletal systems, segmentation, and metamerism complicated the picture as different branches of the ancestral tree diverged.

Invertebrates and vertebrates were treated as two vastly different groups in some ways and may have been a major factor in the annelid theory of chordate origin never getting full acceptance.  The recognition of embryological differences of protostomes and deuterostomes made the presumption of the deuterostome line separating from the protostome line at about the time of the early flatworms a generally accepted view; the speed and ancestry involved in the shift will be shown to differ from the recent views as well as indicating the error of recently accepted proposals.

Time for return of the annelid theory

The annelid theory of origin was a result of the comparison of annelid worms and vertebrates when one was inverted.  When one is inverted and then compared, the arrangement of nervous system and blood vessels and directions of flow are similar.  But the embryological differences seemed insurmountable.  Biochemistry and genetics, as well as greater understanding of embryology and biology made it evident that embryonic and larval features were not a sure guide to determining ancestral paths.  But, as Stephen J. Gould noted in his book (2002.  The Structure of Evolutionary Theory.  The Belknap Press of Harvard University Press, Cambridge, Massachusetts.  1433 pp.), the annelid theory was not revived when the developmental grounds for its dismissal were eliminated.  The developmental grounds do not need to be completely discounted;  they can still be helpful if used with some flexibility.

The inversion the annelid theory encompasses still troubles the investigators below who imply other explanations are needed for the inversion.

Arendt, D., and K. Nübler-Jung.  1994.  Inversion of dorsoventral axis?  Nature, 371:26. 

De Robertis, E. M. , and Yoshiki Sasai.  1996.  A common plan for dorsoventral patterning in Bilateria.  Nature, 380:37-40.

Their efforts are commendable, but unnecessary if the annelid theory is reinstated.  Numerous other reasons to reinstate the annelid theory of chordate origin exist.

Others have not yet shared in my 1983 awakening to the validity of the annelid theory.  By that time it was evident that the Pogonophora were near relatives of polychaete annelids.  But a conflicting paper revived the notion that they were deuterostomes based on embryology.  The article, quote, and notes from my reference file are as follows:

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.  “Both  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 is the article that triggered my (1983 eureka event) awareness of the pogonophorans as the protostome-deuterostome link after initial disgust of their inclusion in the deuterostomes. 

Other factors lend support to the need for reinstatement of the annelid theory with the addition of the Pogonophora as a formerly missing link.  A hint of the overwhelming evidence will be provided in blogs on embryology, inversion, anatomical, and other evidence.

Joseph G. Engemann     June 23, 2013

Saturday, June 22, 2013




There are deep-sea worms that can possibly live longer than a hundred thousand years.  I became aware of this because of my interest in factors responsible for extreme longevity.  I developed that interest from my (1956-1963) doctoral research on a Tasmanian isopod crustacean that takes three years to reach maturity.  A Michigan species from a related isopod suborder can do so in three months.
There are several categories of factors that are responsible for extreme longevity and/or life cycle stage duration differences.  Factors making the deep-sea worm live for thousands of years include.

                Genetics.  This factor is unknown for the deep-sea worm, but is certainly important.  We know insects such as the aphid can produce a generation in a few weeks or less, whereas some cicadas require seventeen years.  Conclusion: the genetic factor can be responsible for great longevity differences.

                Temperature.  In the deep sea temperatures are close to four degrees centigrade year around.  At sea level, temperatures can be more than twenty degrees centigrade higher year around in the tropics.  Many biochemical reactions used by living creatures double in speed for every ten degrees increase in temperature.  The bullfrog may take three years to mature in the northern part of its range, but only need a year in the southern part.  Conclusion: Temperature can be responsible for over two doublings of longevity in the deep sea, over a four-fold difference.

                Extreme pressure.  For partially unknown reasons life processes in the deep sea are greatly reduced.  Depths of 6,000 feet are associated with a 99% reduction of metabolism of bottom communities.  At the pressure of depths beyond 21,000 feet a deep sea bacterium showed a dramatic drop in respiratory rates although other environmental factors were the same.  Conclusion:  abyssal depths could be responsible for a thousand-fold difference in longevity.

                Ecological factors.  These act on the genes through natural selection to make great differences in longevity adaptive to the environment of the organism.  In the comparison I made of Tasmanian and Michigan isopods the magnitude was more than ten-fold within a similar temperature regime.  Conclusion: ecological factors of low food supply, low predation, and stable environment could select for genetics leading to a more than ten-fold increase in longevity.  The pressure and temperature differences noted previously can be multiplied and the result multiplied by this ten-fold increase to make an enormous potential difference for increased longevity of abyssal organisms.

Evolution could be so slow in deep sea organisms that ancestral forms could survive relatively unchanged while descendants migrate to surface waters and change greatly into new groups.  Known examples will be discussed eventually, if I live long enough.  But the major one making revision of the tree of life, as envisioned by my peers, necessary is one of the themes of my 2010 unpublished book manuscript (Evolution Insights).  Parts of it may be condensed in future postings.  The next evolution posting is expected to explain how major errors have been made in proposed evolution of major groups because my peers were not aware of the longevity impact suggested above.

EXTREME LONGEVITY IN THE DEEP SEA, was first implied in my 1968 paper (see references below.  It was later treated on pages 717-732, Chapter 14, of Engemann and Hegner, 1981, Invertebrate Zoology, 3rd edition, Macmillan Publishing Co., New York.  My peers tend to ignore things that are not in major journals, their specialty journals, or monographs.]

Some starting point references, for those reluctant to take my word for it, are:

Brooks, William Keith.  1915.  The Foundations of Biology.  Columbia Univ. Press, New York.  339 pp.   Comments on - the unchanging nature of Lingula (page 219), and p. 217 “the diversity of the Lower Cambrian fauna and of its intimate relation to the fauna on the bottom of the modern ocean”.  See Jablonski et al. below.

Engemann, Joseph G.  1968.  Pogonophora: the oldest living animals?  Pap. Mich. Acad. Sci., Arts, and Letters, 53:105-108.  Extreme age of individuals inferred from published data of others about tube length, probable depth in sediments, and sediment rates of accumulation in abyssal environments.

Ericsson, D. B., M. Ewing, and G. Wollin.  1963.  Pliocene-Pleistocene boundary in deep-sea sediments.  Science, 139:727-737.  Slow rates of accumulation for marine sediments.

Gadgil, Madhav, and William H. Bossert.  1970.  Life historical consequences of natural selection.  The American Naturalist, 104(935):1-24.  P. 12 “thereproductive effort increases with age”; p. 20 “the age for reproduction will tend to increase as the degree of satisfaction or the availability of resources decreases.”

Ivanov, A. V.  1963.  Pogonophora. Consultants Bureau, New York.  479 pp.  This major monograph on the pogonophorans was published prior to the discovery of their giant tubeworm relatives at thermal vents.

Jablonski, David, J. John Sepkoski, Jr., David J. Bottjer, and Peter M. Sheehan.  Onshore-offshore patterns in the evolution of Phanerozoic shelf communities.  1983.  Science, 222:1123-1125.  Fig. 1 shows older groups from shore area are now found in deeper water, older Ordovician inner shelf forms now on outer shelf, Cambrian shore forms now on slope and deeper. Consistent with comment of Brooks, 1915.

Jannasch, H. W., et al.  1971.  Microbial degradation of organic matter in the deep sea.  Science, 171:672-675.

Smith, K. C., and R. R. Hessler.  1974.  Respiration of benthopelagic fishes: in situ measurements at 1850 meters.  Science, 184:72-73.

Webb, M.  1964a.   The posterior extremity of Siboglinum fiordicum(Pogonophora).  Sarsia, 15:33-36.  Fig. 1, page 34, shows “anchor” with 17 setae bearing annulations.  This seldom recovered portion of the worm may be so because the tube portion it is in is deep in the sediments consistent with vertical orientation of the tube.

Webb, M.  1964b.  Tube abnormality in Siboglinum ekmani, S. fiordicum andSclerolinum brattstromi (Pogonophora).  Sarsia, 15:69-70.  When worm posterior protrudes through break in tube it secretes a new posterior tube portion with no annulations but is continuous with anterior portion of the tube and sealed off from old posterior portion; Fig. 1, page 69 shows it for three species. 

Yayanos, A. A., A. S. Dietz, and R. VanBoxtel.  1979.  Isolation of a deep-sea barophilic bacterium and some of  its growth characteristics.  Science, 205:808-810.  It showed rapid depression of growth beginning at depths with pressures exceeding 725 atmospheres. 

This post may have been lost or not published.  I just relocated it and as it is important to the topics I was about to address, I thought I should try to re-post it.  
Joseph G. Engemann, June 22, 2013

Thursday, June 20, 2013



The roots of the animal kingdom and other kingdoms are closely intertwined prior to the origin of multi-cellular plants and animals.  We think the earliest organisms are still represented today by the bacteria and other forms lacking a nucleus in their membrane-enclosed selves.  During this stage, perhaps the first billion years of evolution, the basic biochemistry of life evolved.  The RNA, DNA, and much of the basic materials still found in subsequent organisms evolved.

A consequence of the development of photosynthetic organisms in the world, then lacking oxygen in the atmosphere, was the production of oxygen as a toxic waste product that accumulated and changed the biosphere for the remaining time on earth.  Some of the early organisms developed the ability to utilize oxygen to oxidize organic material for their energy.  They could then remain active in the absence of light while extracting more energy from food than was possible by anaerobic process alone.  

Organisms that protected their genetic material from the oxygen with a nuclear membrane could better survive as oxygen reached higher levels.  Some developed a symbiotic relationship with other organisms.  Details of these early steps are discussed by Lynn Margulis (1981, Symbiosis in Cell Evolution, W. H. Freeman and Co., New York).  The evidence that mitochondria of our cells are a result of symbiosis is very strong; perhaps cilia are derived from flagella that also came from a similar symbiotic origin.

At this stage of evolution the Animal Kingdom or its one-celled progenitors, the Protozoa, had representatives so overlapping with plants and fungi that many biologists prefer to put them in a separate kingdom, the Protista.  These early steps were developing during the second billion years of life on earth.

By the beginning of the third billion years on earth a protozoan that could change back and forth from one with a flagellum to one with pseudopodia had evolved.  Sometime the pseudopodia would develop into a collar around the flagellum.  Eventually some of these dual potential cells stuck together and developed small colonies that eventually specialized into sponges.  The single cell with the capacity for diverse structure and a mechanism for controlling it needed a few control changes in a few different cells of the colony to provide the basic material for evolution of many of the features of all animals.

The Porifera were the first phylum of animals to develop.  They diversified into many different sponge types until one group gave rise to coral-like animals as indicated by the similarity to a Middle Devonian anthozoan (Kazmierczak, Jozef. 1984.  Favositid tabulates: evidence for poriferan affinity.  Science, 225:835-837.).  

Recognition of this evidence of anthozoans as the first cnidarians provides a basis for a simple continuity of phyla in the early stem of animals leading to the next phylum, the Platyhelminthes which may be considered the earliest protostomes.  A simple but unconventional view is that anthozoan polyps gave rise to jellyfish ancestral to triclad planarians.  The complexity of the simple process is why I needed to write my manuscript, Evolution Insights, to make it evident.

The sponges have less well-defined tissues than phyla that follow.   But the main mass of sponge is jelly-like with a few amoeboid cells and a tangle of collagen-like fibers and is much like loose connective tissue in our own bodies.  The jelly-like mass is mostly covered with flattened cells and is perforated by many pores leading to canals and or cavities lined with choanocytes.  Choanocytes are cells with a flagellum surrounded at the base with a collar that collects microscopic food items to nourish the sponge.  Water is passed out one or a few large openings.  Most sponges have spicules.  Spicules are mineralized (calcareous and/or siliceous), often needle-like, or three-pointed and other shapes often specific to the class of the sponge.

The protostomes included all the animals above the cnidarians until the deuterostomes evolved.  The seemingly hidden origin of deuterostomes becomes simple and clear when the role of the Pogonophora is known.  The next several blogs are expected to deal with the origin of the deuterostomes.  Then it will be time to clarify the Porifera-Cnidaria-Platyhelminthes links.  Later, the origin of mollusks and arthropods from annelids will be covered.  The foggiest portion of animal evolution, Platyhelminthes to Annelida, is obscure because the intermediate steps left neither a fossil nor living close relative to my knowledge. 

The annelids seem to be the living representatives of the most ancient animals with a true coelom, a body cavity with body wall lined with a cellular layer of flattened cells.  Organs enclosed in the coelom are also covered with a similar cellular layer; the two layers often connect to form a double layered mesentery.  The mesenteries may help keep organs in position, including blood vessels and nerves servicing them.  Of the simple animals, more complex than flatworms, but still lacking both a true coelom and segmentation (or its derivative, metamerism), although having characteristics more in common with advanced animals, we find only the nemerteans.

The protostomes including flatworms, nemerteans, annelids, mollusks, and arthropods get their name from the embryonic origin of the mouth from the blastopore.  The first (proto-) opening becomes the mouth (-stome), thus their name Protostomia.  In deuterostomes a second embryonic opening or region becomes the mouth.  The deuterostomes include hemichordates, chordates, and echinoderms.

Besides mouth origin, major contrasts between major phyla of the two groups (advanced protostomes and deuterostomes) include spiral versus radial cleavage, determinate versus indeterminate cleavage, presence or absence of chitin.  A minor phylum, the Pogonophora, blurs these and other distinctions and gives good reason to be the link between the two branches of higher animals.  To me, the evidence is so good any other proposals lack standing.  

An earlier post (SCIENCE SCREW-UP NO. 1) provides reasons the currently popular view of phylum relationships is incorrect.  Most of my immediately following posts will address various aspects of the origin of deuterostomes.  

Joseph G. Engemann, Emeritus Professor of Biology, WMU, Kalamazoo.  6/20/2013

Monday, June 17, 2013



Phylogeny, the ancestral tree of species, is often difficult to determine when a species has no closely related species.  Molecular phylogeny was thought to be a source of superior answers to the questions of relationships.  That would be true if all genetic material evolved at the same rate.  But different portions of the genome can have different rates of mutation, so can different species, and the rate can be affected by the longevity of individuals.  So other factors have to be considered to improve accuracy of phylogeny.

The path is determined by natural selection.  Selection may maintain a stable species composition for long times when it is well-adapted to stable environmental conditions.  In a variable environment changes may be relatively rapid over a comparable time period.

Features can be lost more rapidly than they are gained.  The formation of a new structure or a biochemical substance is usually due to accumulation of many mutations.  Many accumulated factors must interact in proper sequence to produce the feature.  But one change may disrupt the entire process.  The change may be fatal if it is an essential feature.  An example, albino organisms may result from one of many possible disruptions leading to a failure to produce the melanin pigment.

Complex features are present in some way in ancestral species.  The eye is an excellent example of this principle.  Some one-celled animals had pigment spots near a light sensitive swelling of the basal part of a flagellum.  The flagellum is a thread-like structure that can undulate; it has internal fibrils in a unique pattern common to cilia.  Variations of the fibril pattern occur in the photo-receptors of eyes of all groups of higher animals with eyes.  The eye structure itself shows variation distinguishing major groups.

Genotypic selection is accomplished through phenotypic selection.  Because genes interacting with environmental factors determine the phenotype (the physical expression resulting from that interaction) many seem to think natural selection acts directly on the genotype.  But survival of the individual is dependent on the success of the phenotype.  Consequently, anatomy and other phenotypic expressions are better guides than genes are to evolutionary pathways in many cases.

Factors causing natural selection can be variable or constant.  They can be characteristics of (a) the physical environment, (b) the biotic environment, or (c) the interaction of those factors.  Ice ages come and go.  Solar radiation is relatively constant, but varies greatly by latitude, time of day, and cloud cover.  Microhabitats vary, such as the side of a tree favorable for moss growth.

Extinction events are typically followed by accelerated evolutionary changes among survivors in the post-extinction period.  The early Cambrian expansion of major phyla is the most remarkable example.

Rapidly evolving species may have greater genetic similarity to descendants of slowly evolving ancestral stock species than to more recently evolved sister groups.  The most dramatic example is the pogonophorans that show up in an intermediate position among other more recent deuterostome clusters.  This aspect of evolution can probably not be found in the scientific literature, since I appear to be the only one that knows about the extreme age of pogonophorans and their connecting link position between annelids and deuterostomes.  Some such suggestion may have been made in a 1978 Copenhagen symposium on the Pogonophora before my 1983* presentation to the Am. Soc. of Zoologists.

Geographic factors are immensely important in affecting the course of evolution.  Continents can act as barriers to marine species dispersal and highways for terrestrial species.  Isolation of groups allows separate evolutionary paths for related forms.

Isolation of marsupials in Australia enabled them to evolve into forms comparable to many of the placental mammals that were so successful on other continents.  The variations in each location are examples of adaptive radiation into new species, while those of opposite groups radiating into forms similar to those in other locations are examples of convergent evolution.

An interesting example of geographic barriers and highways is shown by some terrestrial species found at many different latitudes found at higher locations in the tropics and progressively closer to sea-level as latitudes closer to the poles are reached.  Conversely, some marine invertebrates of shallow coastal seas of high latitude regions are found in progressively deeper waters as they transition to tropical locations.  Temperature is presumably the major factor determining such distribution.

*Engemann, J. G.  1983.  Coelomate animals are monophyletic.  American Zoologist, 23(4):1008. Abstract # 753.  A submission of the complete paper was rejected by an editor of Nature because he considered it to not be of enough general interest.

Joseph G. Engemann      June 17, 2013

Wednesday, June 12, 2013


Darwin and God as shown in his writings

Darwin’s belief in God was something I initially inferred from the last sentence in The Origin of Species.  It was “There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”

The accusations that he became an atheist were somewhat supported by the fact that after attacks by some religious leaders and enthusiastic support of his work by atheist friends he deleted three words from the sentence in later editions of The Origin of Species.  The three words were “by the Creator”, and in the paragraph above, I underlined them.  From his autobiography and letters [the Darwin Compendium, 2005, Barnes and Noble, 1874, including an excellent introduction by Brian Regal] we see the atheist allegation in unjustified.

In an 1876 portion of his autobiography [intended for his children] his writing is informative, for example.  “Another source of conviction in the existence of God, connected with the reason and not with the feelings, impresses me as having much more weight.  This follows from the extreme difficulty or rather impossibility of conceiving this immense and wonderful universe, including man with his capacity of looking far backwards and far into futurity, as the result of blind chance or necessity.  When thus reflecting , I feel compelled to look to a First Cause having an intelligent mind in some degree analogous to that of man; and I deserve to be called a Theist.”

Regarding religion, Darwin wrote in a 1879 letter, that he had never been an Atheist in the sense of denying the existence of God, but that his judgment fluctuated, and more and more as he grew older (but not always) had an Agnostic state of mind.  His son said Darwin “felt strongly that a man’s religion is an essentially private matter, and one concerning himself alone.” 

Darwin, the person

To get a sense of Darwin as a real person with a passionate concern for other, and not a scientist remote from others, a starting point might be to read the last few pages of his Voyage of the Beagle, beginning with his remarks about his August departure from Brazil.  From another angle, his children’s perceptions of him as a father, incorporated in his Autobiography show another personable side of him.

Joseph G. Engemann       June 12, 2013

Tuesday, June 11, 2013



Ecology is the branch of science studying the relationships of the physical and biotic features of the environment.  It is primarily the study of what is happening now with organisms in respect to all features of the world around them.  Ecology goes hand in hand with evolution to give us an understanding of the world around us.

Evolution tells us more about the past and helps us understand the present.  Ecology tells us more about the present and helps us understand the past.  Both can use all other branches of science to contribute to the story.  Basics of ecology combined with the concept of natural selection are particularly valuable to understand the long term course of evolution.


The trophic relationships (or role in the food chain) among producers (mostly plants), herbivores, carnivores, and reducers are fundamental.  If you have not studied ecology you can find out about them in a text such as the one by Dr. Richard Brewer (The Science of Ecology, 1991).  You can find out about his book on his website ( ).  His blogging there has gone more to applying ecological knowledge to efforts to preserve biotic communities.  His most recent book, Conservancy: The Land Trust Movement in America (2003, Univ. Press of New England, Dartmouth College imprint) is a product of that interest.

“Jobs” of organisms in an ecological sense

The hypothetical “ecological niche”, though not necessarily a reality, is a useful concept to understand the history of evolution of biotic communities.  Following extinction events that greatly reduce the diversity of plant and/or animal communities, we find that vacated niches are refilled rather rapidly in an evolutionary sense.  But different species do the job.  The same principle is involved in marsupials providing the kangaroo and other large herbivores in Australia whereas other temperate to tropical lands have had deer and other large ungulates evolve to do that herbivore job.  

The complete story for an organism involves its physical dimensions and interactions with many other properties of the organism and its environment.  Thus as animals first emerged the early ones lacking circulatory systems had to be either very small or flattened or with most active tissues on the surface or perforated or somehow adapted to get sufficient oxygen to all tissues needing it.  As size increased they needed some means of support.  They did not know that, but those that had variation providing such needs out-competed their unchanged relatives.

Multiple functions as a base for evolution of complexity and/or primary function

Many things have more than one use.  This is an especially useful concept to help understand evolution.  An appendage can be useful for one or more functions such as movement, sensory input, respiration, feeding, defense, and reproduction.  One example; when appendages are duplicated on many segments as on an arthropod, selection can eventually result in specializations that differ on different segments.  The principle is one reason biology classes often illustrate the concept with study of a sequence including a worm, a crayfish, a grasshopper, and one or more vertebrates.

My study of isopods showed me an example of how some changes occurring in embryos were based on shifts in a tissue with multiple uses.  The realization that changes can occur in an embryo that are essentially independent of adult evolution made it easier for me to understand the reason behind blogs where I will try to explain the origin of the deuterostomes from the protostomes at the annelid level.  It was an old theory that had been abandoned due to the great difference in the embryology.  I hope to show how the shift occurred.  The Lophotrochozoa-Ecdysozoa error might not have occurred if I had been able to publicize the concept more effectively years ago.

Joseph G. Engemann     June 11, 2013

Saturday, June 8, 2013



One God Many People

I was contemplating the attributes of God.  I don’t know why there is only one God.  But if God is infinite, how could there be room for another?  I’m glad there is only one God.  I don’t have to split my allegiance.  But why are there so many people?

I was taught that we are created in the image and likeness of God.  That’s fine until you wonder about God’s physical traits – a seeming impossibility for a pure spirit.  So I will look for the similarities in other aspects that are not physical.  When I got to humor I had a hard time.  As a Christian, I believe that Jesus is truly God and truly human – quite a mystery.  Trying to relate to the human side of God, I looked for a sense of humor in Jesus.

The Gospel writers may have been reluctant to trivialize the presentation with humor.  It wasn't too long ago that I saw that Jesus was probably having a good chuckle about Peter stepping off the boat and starting to walk across the water to where Jesus was, then starting to sink.  Maybe not, that is a bit like a practical joke.   Maybe the parables were a source of a laugh or two.

I was not satisfied with those explanations.  Now I see God satisfying his sense of humor with us.  Knowing everything that was, is, and is yet to be, the surprise and unexpected connections that often are part of humor cannot be there for God.  But like we get great joy out of a good joke by repeating it and seeing another person’s laughter – we even laugh along with them, shouldn't God also be able to enjoy humor vicariously.  So that may be one reason there are so many people.  

We are bonded to God by his great love for us.  That only increases, if that is possible, his vicarious appreciation of us.  If we exercise our free will and reject God, it is a sad state of affairs.  But if it bothers God, he can easily create another galaxy where billions of others can offer some degree of replacement.  I doubt that that is the way God would solve the problem, but I think I will find out with a very pleasant surprise in the hereafter.

Joe Engemann     June 8, 2013

Friday, June 7, 2013


Science Rules

The rules of science have never been voted on by science in general to my knowledge.  But any systematic investigation of nature and knowledge might be recognized as science if several principles are observed.

Definition of terms is a good starting point.  When terms are agreed upon study of the properties of the subject of investigation can benefit by the accurate sharing of knowledge.  It allows knowledge of the subject to accumulate when it is recorded and dispersed among participants.

Review of the literature is essential to avoid needless duplication of effort beyond the duplication needed to assure the information is correct.  The geometric growth of information has brought the need to get the latest and the best.   The latest is not always the best.  Reading science journals and attending scientific meetings often provokes one into thinking of a further aspect needing research.

Objectivity is needed by scientists.  For a long time, scientific writing was phrased in stilted expressions to avoid the use of the pronoun, “I”.   The hope was that the investigator would be less likely to have a personal agenda that would skew the results.  Truthfulness and honesty are expected of all scientists, regardless of their style of writing.

Methods and materials should be chosen as appropriate for the field of study.  The review of the literature is relied upon to help guide choices.  The materials and methods of laboratory and field researchers may be quite different, especially in biology.

Observations and data accumulated by scientific investigators are the basic materials of science.

Hypotheses are tentative explanations or principles for the results of a study.  They can be promoted to theories or laws if they accurately predict results of additional observations.  A hypothesis should be viewed in competition with all reasonable alternative hypotheses.

Experimentation in its simplest form is manipulation of one treatment variable in a set of observations in the experimental group while a control group has no change or a standard treatment.  Ideally, assignment of members to the two groups should be done randomly.  Statistical analysis of the performance of the two groups can sometimes detect even small differences in results between the two groups.

Results are presented with text, tabular, and/or graphic explanations as appropriate.

Analysis or discussion of data and other aspects may be essential parts of research reports.  Flaws in logic and overlooked implications of results should be avoided if caustic complaint letters to the editor are not desired.

Publication and sharing of results of a scientific study is expected by peers in the discipline.  Typically, results are presented to peers in meetings or some other way of sharing before publication occurs.

Peer review is used to filter information published in leading science publications.  It is done insure accuracy and validity of work submitted for publication.  When peer review is working effectively science benefits.  Some failures of peer review can curtail scientific progress when manuscripts submitted from competing schools of thought are not well evaluated.

Predictability is an implied property of science.  The prime prediction, if is is science it should be repeatable. Other outcomes may be suggested by the results of research.  

For example, my analysis of data of others led me to the probable prediction that life in the abyss of the ocean is extended far beyond other's expectations.  I used the assumption as follows: an excellent study was done of deep-sea brittle stars by Dr. Frank Rokup. His sampling was done quarterly over a year and analyzed as was reasonable for annual changes.  I combined his published data in to one sample, thinking the slow pace of life in the abyss made them equivalent to an instantaneous sample.  The result gave a size distribution similar to some long-lived invertebrates in coastal waters where predation was low.  This seemed to me to confirm my view of extreme age for some abyssal animals.  The graphic results were presented in the last chapter of Invertebrate Zoology, 3rd ed. (Engemann and Hegner, 1981).

Some problems afflict the scientific enterprise

To some scientists, data reigns supreme.  Analysis of data sometimes misses consideration of a reasonable alternative hypothesis.  Methods may not be appropriate.  Precision of technological aspects can exceed application of reason.

Reason got a bad name in science when “armchair” scientists reached their conclusions by just thinking about something when data to answer the question was easily obtained.  Publication outlets and granting agencies often have policies where editorial policy and/or peer review eliminates consideration of research if it does not involve collecting original data.

Meta-analysis and review articles typically do not contain new data.  They are generally done be recognized experts in the field.  Meta-analysis may generate new data from existing data, typically from numerous similar original studies.  That is about as close as mainstream science gets to armchair science. 

The, publish and get a grant or perish, competition in academia has to some extent spurred efforts by scientists.  But the result is often multiplication of publications with small gains and great overlap.  Graduate students can be so important as co-authors to a faculty member’s success that research specialization may interfere with breadth of training.  Production of graduate students may bring rewards to faculty so much that the screening and training of candidates may suffer.  Grade inflation occurred as pleas of those needing educational deferments during wars following World War II seemed to be silently endorsed by faculty.  The overall result of such responses may raise questions about the product of academe.

I intend to have numerous blogs about studies I found flawed.  But that is the way science works.  We get answers that are accepted until a better answer comes along.  Sharing them is a way of seeing how things might be improved.  Even a Nobel Prize winner will make my list of forthcoming blogs.  Is someone out there ready to blog about errors of my views?

Joseph G. Engemann     May 24, 2013  

 Note below added June 7, 2013

I just posted a blog on peer review.  While looking through some old reprints on the peer review process I ran across a review that raised the question, is biology science?  Some of the key qualities of science is that it is repeatable and potentially refutable.  Being repeatable means description of materials and methods is essential if verification is desired.  Laboratory scientists think the controlled experiment is the ultimate in science.  Where does that leave the field biologists whose work is largely descriptive?  One of the reprints raised the question that it might be more philosophy than science.

I don’t subscribe to that view.  The methods of the field biologists do not often have easily described controls.  Their controls may be the norms of other field observations.  Details of the environment can be reduced to controlled experiments, but it then raises the question of what the responses would be in the variables of the natural environment.  When field and lab research overlaps, it is difficult for each side to fully appreciate the contributions of the other side.