Tuesday, September 17, 2019

Final Blog Post

We, the family of Dr. Joseph G Engemann, are grateful for the 90 3/4 years we had him. He left this world on Tuesday, September 10, 2019.

Here is a link to his online obituary: https://betzlerlifestory.com/obituaries/joseph-g-engemann-phd.128626

We hope that his posts will be maintained in perpetuity, and that his thoughts and contributions will inspire current and future generations of those studying evolution.

Saturday, June 8, 2019

The "Great Dying"

An NPR report by Christopher Joyce in the cell phone news reported earlier this week related information about a Smithsonian exhibit's information related to the greatest extinction event known in the history of the earth.  The end of the Permian event about 250 million years ago nearly extinguished life on earth and was referred to as the "Great Dying".

Volcanic activity, with probably some help from asteroid impacts, reduced ice cover and made atmospheric pollution increase global temperatures far beyond the state we now have.  Cold climate animals could no longer survive in the arctic regions where they may have thrived on the land mass prior to its breakup into the present continental condition.

Surface temperatures and absence of polar ice made the cold water input to the ocean bottom stop, or be very slow to replace the bottom water, but the hot surface water would become hotter and make a thicker layer.  Water from polar regions would presumably be warmer and lighter than abyssal water, although colder than water from most of the ocean.  That water would have an intermediate density that would replace water of similar density under or in the thermocline.  The abyssal depths of some ocean basins away from asteroid impact would probably remain relatively unchanged and give refuge from the "Great Dying" to pogonophorans and other species that would provide life to shallower waters after conditions improve.

The end of Permian extinctions were the worst of the Paleozoic Era and exceed the species deaths of the second worst extinction episode at the end of the Mesozoic Era's Cretaceous Period about 65 million years ago.  Pre-Cambrian extinctions may have been more deadly in the two billion years of Pre-Cambrian life, but it is unlikely for much evidence to survive geologic processes.


Reports of high rates of oxygen consumption by microbes deep in abyssal sediments seem to be impossible and require a different explanation, although thermal vents and heat from magma could have some interesting physiological implications of which I am unaware.

The rapid growth of giant tubeworms at thermal vents seems dependent on chemosynthesis by bacteria in special tissue as a source of nutrients; like normal pogonophorans, giant tubeworms lack a functional gut.

The reduction of diffusion in water under great pressure that I have suggested as the explanation for the dramatically slow aging of deep sea organisms would seem to be greatly modified at higher temperatures of thermal vents and presumably deeper sediment warmed by the core of the earth if the reported  rates are correct.

The abyssal region remains a refuge under siege from plastic and other pollution that may survive our worst climate-altering assaults if anyone will be around a few million years from now to notice.

Joe Engemann    Kalamazoo, Michigan    June 8, 2019

Wednesday, May 29, 2019

Spiral to Radial Cleavage Transition

Another index card accompanied the one described in the previous post, suggesting the protostome / deuterostome move of retinal nerve fibers from behind the retina to in front of the retina, can be a result of the dorso-ventral inversion mediated by the Pogonophora.  This additional card was written on 1/28/2003 and included the following two statements.

"Somewhere between 10 PM last night and 11:30, I was thinking about the Asellus egg appendage example of embryonic evolution as a model for the embryonic evolution of protostome to deuterostome.  It occurred to me that it was a better example than I thought, it may have been for embryo survival, not just metabolic speed for development."

"Progress seems to have resumed since I started.  45 years with the other explanation:  If I am so creative, why didn't I think of it before in those terms?  I guess I am not,  I'm like everyone else!"

Why I didn't think of it was almost certainly a result of being overwhelmed with the appendage appearing as a new evolutionary feature of the embryo, and it was not an adult ancestral feature that was incorporated in earlier stages as the abandoned "biogenetic law" would have predicted.  In a way, the appendage did incorporate an ancestral feature such as one found in the more primitive Tasmanian isopod as a yolk-filled bulge evolved into an appendage.  Although the appendage disappears in the adult isopod, its position makes it a model of a possible base for development of wing precursors in ancestors of insects.  The only certain fact is it shows embryonic features can arise without representing a precursor in adult features.

The reasoning for the spiral to radial transition is speculative but thought to be almost certain because other evidence (1) puts Pogonophora between protostomes and deuterostomes on the tree of life; (2) shows loss of features can evolve more rapidly than gain of features; (3) the deep sea nutrient input is impoverished; (4) reduced egg-shell thickness and loss of early cell specificity are both energy saving developments of deuterostome development. 

Point one above shows us the protostome condition was ancestral.  The deuterostome condition evolved by loss of specificity in early cleavage divisions of the fertilized eggs; this may have been due to weakened thin or missing eggshells not providing rigid spatial relationships and signals for development.  Loss of such signals made each early division product express the entire genome needed for the "twinning" seen in deuterostome eggs.  Cell fate is eventually determined in some deuterostome embryonic tissue as shown by grafts of presumptive leg tissue making additional legs on frogs.  But that development may require an interaction of cells in the tissue since the example of cloning individuals from skin cells indicates each cell must have the entire genome.

More primitive protostomes that have the ability to regenerate tissue or reproduce by fragmentation must have complete genomes in such cells.  Notable exceptions are aschelminths such as nematodes that undergo reduction of the genome in cells other than reproductive tissue cells.

Simplification via pogonophorans is multi-faceted and simultaneously driven by selection for survival in abyssal conditions and survival during episodes of drastic species extinction during periods of asteroid bombardment

A.  The pogonophorans, as noted above provide a rational explanation for major distinction of the origin of deuterostome development.

B.  Pogonophorans provide an answer for the puzzling inversion of systems noted between protostomes and deuterostomes.

C.  Pogonophoran abyssal adaptation makes their survival during major extinction episodes easier to understand, especially due to their extremely low respiratory rate, extreme longevity, and ability to absorb nutrient at levels found in abyssal sediments.

The pogonophorans become an evolutionary bottleneck limiting features of deuterostomes

A.  Hemoglobin is the only respiratory pigment in blood of deuterostomes.

B.  Chitin is reduced in pogonophorans and absent in deuterostomes.

C.  Segmentation is reduced in pogonophorans and absent in deuterostomes, although metamerism is functionally present as a base for deuterostome complexity development almost certainly derived from ancestral segmented features.

D.  The bottleneck entry was via ancestral polychaete annelids.  The bottleneck exit to the chordate line was via hemichordates.

Complexity seen in deuterostomes is probably based on the limited genetic inheritance from the pogonophorans via duplication of gene copies going on to functionally different units.  At the same time some older versions may be eliminated due to the vagaries of natural selection.

The extreme longevity I first suspected, from the depth pogonophoran tubes must reach in abyssal sediments, seems confirmed by the long-branch attraction shown by pogonophorans appearing in genomic clusters of phylogenies of other major groups.

Joseph G. Engemann    Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan   June 29, 2019

Friday, May 24, 2019

Pogonophora "eye"?

For many years I carried 3 x 5 cards in my shirt pocket so I could jot down things I wanted to remember or explore.  I just came across the following one recently; it was tucked in with some other paper's.  Read as follows.


1/16/2003  Jan 16, 2003  JGE idea

1   Pogonophora "eye" as possible intermediate in having retina reverse molluscan condition

2   Pogonophora (nearly) "straight line" in evolutionary tree with Pre-Cambrian divergences of other groups at various Post-extinction events

3   TATA box distribution


On the back of the card I had only a black spot and an x spaced about two inches apart.  the spot and the x are a simple device to demonstrate our blind spot where the optic nerve goes through the retina.  By closing one eye and looking at one mark about six to ten inches in front of your open eye and maneuvering the card until the other mark disappears in the blind spot when the brain fills in the void,

If the x in on the right and I look at it with my left eye, the dot disappears about six inches from my eye when the marks are almost horizontal.

The squid eye does not have a blind spot because the nerve fibers from the retina lie behind the light sensitive retinal cells.  All vertebrate eyes presumably have a blind spot because the nerve fibers from the retina run over the retina until they form the beginning of the optic nerve as they pass through the retina.  There, the blind spot is not apparent to us because the other eye fills out the image in the brain.

The Pogonophora must have retained enough of the eye genes to provide a base for rebuilding the eye.  But the inversion as compared to the annelid, mollusk, arthropod line made the light sensitive retinal cells and the nerve fibers reversed in position.

TATA box things would be worth examining if you are a molecular biologist looking for answers to some related evolutionary steps.

Pineda et al., 2000, Proc. Natl. Acad. Sci. USA, 97:4525-4529, say "previously demonstrated expression of Pax-6 in planarian eyes, suggest that the same basic gene regulatory circuit required for eye development in Drosophila and mouse is used in the prototypic eye spots of Platyhelminthes and, therefore, is truly conserved during evolution."

Joseph Engemann   Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan    May 24, 2019

Monday, April 1, 2019

Surviving Extinction


The pre-Cambrian asteroid bombardment may have been preceded by more spectacular episodes that delayed the evolution and entry of larger organisms into the perilous environment of earlier times.  Successful organisms would be dispersed in most directions and become established to spread the range of those species.  At the same time on the periphery of the range variation and natural selection resulted in new species when changes made them reproductively isolated from the ancestral ones.  Well established ones would outcompete and/or expand the range.

The deuterostomes may never have evolved without the drastic environment of the early asteroid bombardment.  Pogonophora are probably ancestral to all deuterostomes.  Protostomes probably include many groups whose separation from annelids ancestors was prior to, at the same time, or later than the separation from annelid ancestors of the first deuterostomes, the pogonophorans.


Many factors that contribute to survival are of value in reproduction and/or dispersal.

Lucky locations
Regions remote from impact may have had caverns, sediments, isolated aquatic habitats and other locations where survival of cysts, eggs, hibernating stages, or other mechanisms enabled survival.  Perhaps ice shelves in polar seas protected organisms beneath them.  Perhaps marine forms drifting down to death were sometimes lifted back into survival depths by a later impact at the end of bombardment.

Fat and some other tissues can be utilized to maintain life during periods of starvation.  An extreme example of degrowth is shown by some jellyfish that are capable of absorbing reproductive organs and regressing to earlier life stages as they grow smaller.  They may be able to do that in successive seasons as they drift from nutrient rich bays to open oceans with less food and back to nutrient rich locations; the cycle could be part of the annual cycle of productivity.

Absorption of dissolved nutrients
All phyla tested, except arthropods, have shown the ability of some species to absorb amino acids from dissolved amino acids in water at some stages of their lives.  The ability to take up dissolved organic matter from seawater is a particularly important method of nutrition for species having eggs with little yolk that hatch before feeding organs are well-developed.  The arthropods, with their chitinous exoskeleton, are not equipped to get nutrition via absorption of dissolved nutrients nor have useful degrowth; this may have been part of the reason trilobites became extinct at the end of the Paleozoic.

Resistant stages
Overwintering eggs of arthropods such as many insects, fairy shrimp, and perhaps many other animals have the ability to repopulate a habitant after adults die from winter freezing or ponds dry and refill.  Freshwater sponges produce asexual cysts (gemmules) that have similar use.  Such stages are often an important dispersal mechanism for organisms to reach new habitats via mud on water bird feet, or on mammal fur.  The stages may survive a trip though the digestive tract during dispersal.  Such mechanisms were probably partially selected by the value of providing a new generation into the areas of greatest damage after an extinction event before others lacking such a survival mechanism arrive and become competitors or predators.


The abyssal portion of the ocean is the most widespread area of the earth and the depth and stratification of the overlying sea make it likely that much of it would be relatively untouched by an asteroid or two sending catastrophic waves over land and shallow seas killing most organisms that did not have protected refuges (caves or burrows etc.).  Those not destroyed still had to find food and other requirements for survival.  The peak of bombardment was followed by a reduced supply of remnants of the fractured planet that occupied the zone between Mars and Jupiter.  One big one, like the last one the helped finish off the dinosaurs, produced many extinctions and opportunities for newly evolving species to take over roles of the extinct forms.

The pogonophorans would continue to expand range and send descendants into new areas.  Other groups would also be testing new environments, for example, the crinoids appear to have had adaptation to abyssal conditions and retained many of the adaptive features after repopulating the shallow seas after the worst of the bombardment was over.  Pogonophorans have been found in a few locations in sediments only a few hundred feet deep, but the many vertebrates and the connecting groups diverged from their common ancestors almost a billion years ago with origins at various depths and locations where some stability of the environment with hospitable conditions existed.

The specificity of environmental adaption for deep sea animals has been shown by the limited range of a few hundred meters isolating similar species to nearby depressions surrounded by other related species encircling the surrounding abyssal area.  Such environmental specificity should not be a surprise when you see how uniform the alpine limit of the tree line can be.

Some key features that enabled pogonophorans to survive in their abyssal habitat included:

A very slow metabolism compatible with survival on sediments receiving very little nutrient input in the form of amino acids from slowly decaying organic debris (perhaps supplemented by surface waters raining down organisms killed by the surface disturbance).

The depth of their tubes enabling survival from attacks by predators.

The slow reproductive rate and growth rate allowing reproduction hundreds of years after the worst of conditions.

Their hemoglobin and circulatory system enabling adequate oxygen to be stored and or transported to the posterior end where nutrients were absorbed in anaerobic sediments.

Planktonic larvae capable of dispersal over great distances and time to repopulate large devastated areas of sea sediments.  Those that did not progress to shallower seas are still much the same as the pre-Cambrian ancestral stage of the line ancestral to chordates.

Joseph G. Engemann   Emeritus Professor of Biology, Western Michigan University
 Kalamazoo, Michigan     April 1, 2019 (no fooling)

Tuesday, March 19, 2019

Pogonophora - Central position in evolution

Pogonophora: Their spectacular role in animal evolution

A spectacular connection of the two main higher animal groups

Early embryology of the two main lines of animals

     The Pogonophora show how the radial and indeterminate cleavage of deuterostomes (echinoderms, hemichordates and vertebrates) came about from pre-Cambrian annelids in the deep sea while other annelids retained the spiral and determinate cleavage of protostomes as they were giving rise to arthropods and mollusks.

     The deep sea had low input of nutrients that put a premium on not investing in heavy egg shells that protected eggs of protostomes as they were confined in the spiral pattern of cleavage, a confinement that was released by less confining outer membranes that allowed a more direct radial cleavage pattern.  At the same time radial cleavage did not produce the immediate cell fate into a particular tissue, thus making possible more than one viable embryo from a single egg as each of the early cleavage cells retained all of the development potential of the original egg.  The ability to complete development without all the original cleavage products had high survival value in the rigorous deep-sea environment, although details are speculative.

    My comparative study of Tasmanian and Michigan isopods included observation of the impact of the egg membrane’s role in confining development, leading to a unique egg appendage, a clear indication that evolution can occur in developmental stages independent of adult development.  (see more on “Origin of deuterostome embryology” in blog post dated 6/24/2013)

Systems inversion

A simple process

The inverted position of blood vessels, nerves, oral openings of deuterostomes as compared to protostomes (especially the ancestral annelids of both groups) was proposed as evidence of the central role of annelids in evolution of higher animal phyla.  The original reason for rejecting the theory was the drastic difference in early embryology of the two lines of animals.  The next reason thought to negate the annelid theory as well as the embryological argument against it was the use of nucleotide and other molecular data.  Such data must be realigned taking into consideration the effect of the astronomically slow rate of genetic change in the pogonophorans ancestors.

Inversion, the first step

The inversion of annelids began with certain polychaetes that began living vertically in tubes they secreted, as seen in Sabella and many other shallow water polychaetes.   As those growing in progressively deeper water, with less food, became dependent on absorption of nutrients in pore water of the sediments they outcompeted those wasting energy on producing a mouth and some bilateral structure.  This stage is still found in abyssal pogonophorans. 

Inversion, the second step

The return of descendants to shallow seas occurred once the worst episode of pre-Cambrian asteroid bombardment eased.  As they arrived in shallower more nutrient rich areas, they reformed the remnants of their digestive system with a new mouth on the former dorsal side which became the ventral side, as they groped around the sediment surface near their tube, finding food particles that pushed the epidermal and gut layer together triggering mouth formation on the former dorsal surface without the restriction of the nervous system that originally had encircled the esophagus.  Other clues to this step are presented by the parallels of endocrine hormone function, transport, and structural similarities of vertebrates, arthropods, and annelids.

Protostome-Deuterostome links


The segmentation of annelid type was found on a short portion of the most deeply embedded part of some pogonophorans; it included setae that are a very annelid like characteristic.  A few anterior regions are noticeable but without the posterior segmented region it would be difficult to make an annelid connection.  The metamerism of chordates such as ourselves seen in bone, muscle, nervous system and blood vessels is now easily understandable with the intermediate stage of pogonophorans.
The transition from pogonophorans to chordates is best shown by the larval stage comparisons of pogonophorans and hemichordates.

Molecular evidence

Molecular features of several types show greater similarity between deuterostomes and advanced protostomes than their earliest variants found in more ancient protostomes once thought to be the closest common ancestors at the protostome-deuterostome split.

DNA/RNA studies of evolutionary relationships at the phylum level need reevaluation because major ones have ignored the mutation rate differences associated with generation times.  Many well focused studies have shown generation time does affect evolution rates.  One impact has been the Pogonophora showing up in many odd places in phylogenetic trees because they are almost unchanged since their divergence from major groups that have diverged even more from more recent relatives.

Six other posts, from June 17 to June 20, 2013 have additional clarification of the points made above.  The second June 30th post of that year is an annotated bibliography that has some emphasis on protostome/deuterostome comparisons.

Joseph Engemann   
Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan    May 19, 2019

Monday, March 4, 2019



The environment makes no conscious effort to select traits of an animal or plant beneficial to itself or the organisms resident in its habitats.  If the location is in a suitable part of the range the animal occupies, it can contribute to survival and reproduction of the animal, especially of genetic variants having the genetic features best adapted to the environment.  An animal may select the environment, although it may not be a conscious act.  Foraging to new areas is less likely to occur when food and housing are abundant so a search does not take the organism to new areas.

Some examples of how the environment passively results in natural selection of animal features you are already familiar with-
      the streamlined shape of fish (and birds), tapered at each end so resistance to movement through water (air) is minimized.  The obvious exceptions, as in baleen whales, occur when feeding or some other benefit is more important in their lives.
     coloration blending with the visual background.  Again, exceptions occur when attracting a mate or warning predators of your toxic properties is more beneficial to survival.
     fur or feathers aiding temperature regulation at the same time providing physical protection such as abrasion resistance, flotation, and a mechanism for seasonal color change.
     appendage modification improving function for climbing (claws), digging, feeding, and locomotion to name a few.


A less familiar example, unless  you have a background in evolution and marine biology, is the difference between the cartilaginous and modern bony fishes and the role of air breathing fish in the evolution of bony skeletons.  Survival of fish in anoxic ponds or ones that temporarily dried up, selected fish having more mouth surface able to extract oxygen from water or air.  Ultimately, a pocket becoming the lung of lung fishes, then of amphibians and eventually reptiles, birds, and mammals in one line and from the fishes the early lung was adapted to the air bladder/swim bladder enabling evolution of the modern bony fishes.

It is interesting that the bony fish in the ocean had their origin in fresh water.  Sharks and other cartilaginous fish do not have fresh water fish in their ancestry.  The flotation provided modern fish by the air bladder offsetting the extra weight produced by bone, as compared to the weight of sea water, is partially provided by oil and/or fat stores for cartilaginous fish for excess of weight of bodies heavier than sea water.  Some compensate by continuous swimming providing "lift" from wing-like pectoral fins or body shape.


The deep sea abyssal region and subterranean aquatic environments have both similarities and differences.  The similarities usually include absence of light, stability of temperature, no green plants, low input of food, low predator density, cool temperatures.

In response to those features of the environment there is no selection eliminating loss of vision, pigmentation, and defensive weapons.  Slender, elongated appendages provide some adaptation for loss of vision,  They may also enable walking on soft, unstable sediment accumulations and sensory input for feeding.


The abyss
Soft sediments dominate abyssal environments and currents probably cause less erosion and relocation of sediment.  Temperature away from thermal vents are slightly above the freezing temperature of water.  Invertebrate species present are from major groups first found in sediments from older sediments that were in near shore environments (Jablonski et al., 1983;  see references at end of the June 22, 2013 post of this blog).

 This trend to migrate to deeper water and newer related groups evolve in shallower sea areas was not documented for abyssal species but seems to be a reasonable projection.

Temperate Zone Caves
Numerous instances of cave dwelling crustaceans were originally lumped into one or a few species with what were thought to be their closest relatives in other caves.  Later research showed their closest relatives were in surface waters adjacent to the caves; the rapid adaptation to cave dwelling led to similar loss of pigmentation and vision of less value in showing their evolutionary origin in post-glacial times.  This is one example of how rapidly evolution can occur to bring about the loss of characteristics of little use but essential to survival in a different environment.

notes the factors thought to be responsible for slow metabolism and increased longevity in abyssal animals.  I speculate that the slight compression of water at great depths decreases molecular mobility and so called Brownian movement noted with oil immersion microscopic viewing of cells and related particles; this could be a major factor in the slow pace of life and evolution in the abyss.  I have not searched the literature for related research for many years,  One suggestion in an older article about pressure interference with cell activities was the variable rate of compression of organic compounds could stop or reverse the direction of action toward the product most greatly compressed.  If so I would think alternative metabolic pathways might evolve, but oh so slowly under abyssal conditions.

It seems to me that it would be simple for a physicist or chemist with access to equipment with extreme pressure to compare the rate of diffusion from a grain of dye, or the rate of sedimentation of fine particles, or both to a range of pressures. ( see blog noted  above for reference to Yayanos, Dietz, and Boxtel 1979 study of pressure effects on growth)

My nebulous account of factors enabling understanding of the pogonophoran story is, unfortunately, not easily told in a concise way.  The scattered threads that lead to understanding of the story is perhaps inaccessible to many viewing one of the disconnected bits I provide.  It took a lifetime for me to see the things I present.  I hope others do it more easily and find the trip interesting.  If you see what I am attempting to say, I encourage you to point it out to Wikipedia.  You will need to include a few scientific journal references noted elsewhere in this blogsite to have any hope of others resisting the urge to expunge the entry as not being in sync with existing views.  It is normally good, but preserving the status quo can be a major stumbling block to creativity.

Joseph Engemann     Kalamazoo, Michigan      March 4, 2019