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 I 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 secies 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

Tuesday, February 12, 2019


Thinking that my days are limited made me want to make sure that the things I have  to contribute to understanding the major features of the evolutionary tree of life are passed on to the next generation.  I think this blogsite has enough information to do the job if it is studied by a well-trained biologist.


Others apparently have found the 2/17/15 post on the body cavity of interest since over half of the pageviews each month are to that post.  I suspect it is assigned reading in some classes on several continents because of the clustered nature of the country sources of the views.  The post was included almost as an afterthought to supplement coverage of evolutionary discussion of body systems.

Its major interest to me was the minor bit about formation of openings where layers of bare ectoderm and entoderm cells meet.  That can help one understand the new location of the mouth of deuterostomes when the connecting link, the pognophorans, emerged upside down (compared to protostome ancestors) as they re-entered coastal waters following extinction events.  The resulting inversion of systems of deuterostomes, as compared to protostomes, was discussed in the post dated June 28, 2013.  This process enabled fusion of ganglia to a compact brain close to sensory inputs of a head in an anterior position enabling short and speedy neural connections as the owner probed the environment.  Perhaps this phenomenon is best illustrated by birds and their ability to fly through a sea of tree branches.


Structure of the ocean and its physical state under great pressure needs to be understood to see how the pogonophorans can survive the many generations virtually unchanged in the deep sea while their wandering descendants evolve to produce the deuterostomes in shallow water.  Several old and some recent posts address this issue.  The common ancestry of all deuterostomes with a close relative of the earliest annelids explains why nucleic acids produce odd results in some erroneous molecular phylogenies.  The results are only odd because they complicate phylogenies calculated with invalid assumptions of uniform rates of genetic changes in evolution.


These tubeworms represent survivors of an evolutionary bottleneck, the deep-sea, where they developed a new type of embryonic development (or cleavage), lost blood pigments other than hemoglobin, and lost the ability to make chitin in the stem group leading to vertebrates.

The blood vascular system was needed to store and transmit oxygen to the portion of the worm embedded in anaerobic sediments.  A functional digestive system was reduced to near disappearance and it reformed in a way that did not penetrate the brain in descendants moving to shallow sea areas.


It is counter-intuitive to give importance to regressive evolution when we think about the grand scheme of evolution going from the first small cells to the diversity of size and complexity of the world of life today.  Simple to complex, or progressive evolution, is the explanation our intuition provides.

So the loss of a functional digestive system seems counter intuitive and hard to accept as a way forward to the vertebrate gut from the "degenerate" pogonophoran reduction or loss.  Paleontologists found the simple to complex markings on certain cephalopod shells actually went from complex to simple as the fossil record was better developed in their collections.

In regressive evolution, the regressing feature may be targeted for loss indirectly by the better survival of organisms that no longer need the feature; any mutations causing less nutrients to go to such a feature leave the organism more for better reproduction.  The speed of regressive evolution can be much faster than progressive evolution.  Both can be happening at the same time.

The largest animals are a remarkable example of regressive evolution in the whale's adaptation to aquatic life.  All that process of evolution through four-legged ancestors to some with remnants of leg bones no longer used is one example of loss or regressive evolution while other adaptations are evolving.

The annelid worms provided an important feature in our evolution by the segmentation or metamerism producing a series of duplicated structures that could produce different structures in different parts of the body.  The phenomenon is graphically illustrated by the appendages of the crayfish in the protostome line of animals.


We share many molecular features with other organisms.  Nucleic acids and biochemistry of energy production are even shared across kingdom boundaries.  More specialized biochemical functions often are shared by coelomate protostomes and deuterostomes having closely related compounds although simpler molecular versions may also be found in more ancient protostomes.

Neurosecretions, biochemistry of vision, and biochemistry of metameric processes have similarities that help make the pogonophoran link of deuterostomes to protostomes much more obvious than is generally recognized.


Pogonophorans are the only animals with structural features demonstrating the transition from annelid to deuterostomes.  They explain the importance of their deep-sea life in the regressive evolution leading to a new type of embryology in the deuterostomes, their survival during extinction events, their extremely low metabolic rate enabling long life and slow evolution in the impoverished environment of the deep sea.

Joseph G. Engemann      Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan            February 12, 2019    (Happy 128th birthday, Dad)

Tuesday, January 22, 2019

Trump Evaluation Quiz

Throw the rascals out-

seemed to be the creed attracting the Trump followers.  There was some value seen to rooting out entrenched legislators who appear to be at the beck and call of money and power brokers.  But the cure turned out to be worse than the disease.  Bi-partisanship seems to have vanished with the death of John McCain.

The art of the deal seems to consist of insults, lies, extortion, deceit, and bribery.  Trusted authorities are those who agree with you.  Sometimes it seems Fox News, Rush, Sean, and Kelly may provide unbiased analysis so I can't automatically condemn their statements.  A Trump deal appears to be a solution tailored to his request.  His imposition of a government shutdown looks like an attempt to extort money for the wall from congress.  But he probably won't accept any compromise until the lack of funds ends the FBI investigation of his alleged wrong deeds.

For each topic below, read the statements under the topic heading,  Then on the line in front of the topic enter a "T" if the statement(s) is (are) true; enter an "F" if the statement(s) are false or fake news.


Trump started debates of presidential contenders of his party by focusing on the one he probably thought was most vulnerable to nasty comments.  He continued to pick off others, often minimizing their strengths as failings.  Insults are readily applied to those opposed to any view of his.

_____ LIES

His tweets on Twitter as well as more formal presidential statements are full of self-contradictions,  It seems that any thing supporting or opposing a particular view could be documented by his utterings.  Is he guilty of lies, memory lapses, mental processing failures, or some combination of all of the above?  His lies directed at others often seem to be projections of his own failings.


The government shut-down is his doing.  He seems to think blaming democrats for it will make them agree to his demands.  That it is a ploy for something else seems indicated by his stomping out of a meeting he arranged with two congressional leaders.

_____ DECEIT

Circumstantial evidence points toward keeping his income statements under wraps so profiting from bankruptcies, Russian contacts, and shady deals won't be seen.  Unreported control of foreign financial accounts could be evident and lead to unreported campaign financing.  I thought he talked a lot about Hillary's email and other problems before they were publicized and before the Russian influence  was evident.  It was easy for me to think he had advance clues from them, perhaps from suggestions he dropped.


I can't believe his lawyer took care of his girlfriend problems without some instruction.


His off-the-cuff remarks show little sensitivity to humans.  His reading from the scripts his speech-writers put on the teleprompter make me think he is a sensitive person.  But tweets confirm the insensitivity and lack of appreciation for anyone of other sex, race, national origin, political view, and not visible in his mirror.  If it were not for this problem we would have far fewer children separated from their parents, fewer people born in this country and living admirable lives while facing deportation.

Results     5 or 6 T's, watch Fox News sometimes;  5 or 6 F's,  watch CNN sometimes; 3 or 4 T's or F's, its a puzzling world, isn't it.

Other than the above, and messing with medical care, the economy, foreign relations (did you see the recent clip of his elbowing a head of state out of the way so he could be front and center of a photo-op during a foreign meeting?), and causing an exodus of experienced leadership in government departments-  well, other than that he isn't doing bad and God still loves him.

Joe Engemann    Kalamazoo, Michigan      January 22, 2019

Thursday, January 17, 2019

Variable Rates of Extinction and Evolution

A New Theory?

While composing the previous post about the status of survival/extinction of the Tasmanian tiger I thought of the impact of impending extinction on rates of evolution.  It may be discussed in literature I am not familiar with, but it was new to me; perhaps the first new idea  about evolution that I have had in ten years and certainly the first since I turned ninety last year.😊

The theory of "punctuated equilibrium" in rate of evolution proposed by Gould has largely been abandoned as variation caused by probable artifacts of sampling problems faced by paleontologists.  The assumption of a uniform rate underlying known variability around such a rate has been accepted by many molecular phylogeny researchers and caused the errors in our understanding of the relationship of major phyla to one another as shown by the sixth post on this blog site posted 5/31/2013.

The Tasmanian tiger

Maybe it is extinct, maybe it is surviving in remote areas of Tasmania and/or continental Australia.  But the bounty on them in Tasmania reduced them to such a small population that there has not been accepted evidence of them in the past few dozen years.  Could some have learned to avoid inhabited areas or developed excellent ways of avoiding human contact?  Not doing so could have eliminated those lacking such skills during the time the bounty was effective.

Genetic diversity

A reduced population makes it likely that some genetic diversity is lost and thus adaptability and the chance of surviving becomes more limited, possibly causing further loss of genetic diversity and ultimate extinction.  Extinction from such an event is not as dramatic as extinction from natural disasters such as asteroid impact, disease, introduced predators, climate change, and evolution of better competitors.

The ecology of extinction and expansion of range

There are many causes of both factors.  In a stable environment competition is a major factor as some balance is reached if the less well adapted species can specialize in utilizing a part of its environmental resource of food and housing more effectively or, alternatively, utilize a greater range of resources.  Migration and other factors may also be part of the equation.

Either being a specialist or a generalist can be an effective way of competing for survival,  The generalist probably will yield a greater diversity of new specialists following a major extinction event.  The best specialists may also do well and dominate in the same post extinction time.  If overspecialization occurs a species may become extinct earlier during a major extinction episode.

Species differ in their habitat requirements.  Large predators typically require large suitable areas.  Fragmented habitat may make life difficult for many species although connecting corridors of suitable habitat can help survival.  The prey species of predators also have their special requirements.  For the Tasmanian tiger, life may have been difficult to sustain because many of the medium sized marsupials of forests are adapted to tree-dwelling.  Kangaroos and larger wallabies are more likely be in more sparsely forested habitats.

Human activities would seem to be generally detrimental to survival for many species.  Besides our causing reduction of favorable habitat, pollution, introduction of pest species, and our general lack of awareness of the damage we do should put us in awe of the survivors.  The good that we do by providing some food at critical times can be canceled by the danger feeding stations provide for disease transmission as well as sites attracting predators.  The natural spacing of species and their survival is more likely to be enhanced by well-designed land conservancy programs.

In retrospect, I do not have a new theory, it is just awareness of the complexity and breadth of application of existing ones.

Joseph Engemann    Kalamazoo, Michigan     January 18, 2019 

Tuesday, January 15, 2019

The Tasmanian Tiger, Extinct, or Not?

The uncertain state of affairs

The question of exinction of the Tasmanian tiger (the thylacine) was raised in an interesting article, "Paper Tiger" (Brooke Jarvis, The New Yorker, July 2, 2018, pp. 44-54).  According to Jarvis, the last one in captivity died in a Hobart, Tasmania, zoo in 1936.  That was twenty years before I arrived and was mentored by Dr. Eric Guiler, an expert on many Tasmanian zoological topics, during my year as a Fulbright scholar at the University of Tasmania.

On several field trips with Dr. Guiler (see endnote), and others by myself, many other animals or their sign, such as tracks or droppings were seen.  But such lack of evidence is not very convincing because- such rarities as the Tasmanian devil and the platypus I only saw in zoos, Michigan mammals known to exist but seldom seen outside of zoos include badgers, bobcats, cougars, flying squirrels, mink, and otters.

It seems reasonable that with the bounty put on tigers, to reduce their predation on farm animals, their numbers may have been reduced beyond their ability to survive.  But Tasmania has much uninhabited potential tiger habitat where few would have chances to observe them.  Some suspect that some may still survive in wild country along the north coast of the Australian mainland.  Both are plausible, but seem to require better documented evidence than is presently known.

A few potential factors

In favor of their non-extinction is the possibility those most adapted to avoiding humans may have left some survivors.  Anecdotal reports would seem to support this view.  But the ease for humans to see what they want to see has caused the shooting death of numerous hunters and a few cattle during the hunting season in Michigan; eye-witness testimony is of questionable reliability.

Extinction is perhaps more likely when numbers are greatly reduced.  Habitat reduction is one cause.  But small numbers may increase inbreeding and thus increase the likely of mortality due to deleterious genes.  Small numbers can also interfere with opportunities for mating and consequent reproduction.  Other factors may also operate if social learning is involved, although I have not heard of Tasmanian tigers forming packs.

Extinct or not, it is still an open question.  Negative facts and hypotheses such as extinction are very difficult, if not impossible, for a scientist to prove.

endnote: Dr. Guiler is the one standing to the left in the picture in post number 51 -

Joseph G. Engemann      Emeritus Professor of Biology    Western Michigan  University, Kalamazoo, Michigan       January 15, 2019

Monday, January 7, 2019


There seems to be a burst of energy put into discovering new species that add to knowledge of the diversity of life in the Cambrian and earlier fossil fauna described in Gould's book about the Burgess Shale deposits in the Rocky Mountains of Canada.  A recent issue of Science summarizes the results of the summer fossil collecting season of an additional site not far from the Burgess Shale site.  Additional sites, especially in China, are major locations of fossils from the same general time over 540 million years ago,

The discoveries are largely more of the same - arthropod groups, some now extinct, and some ancestors of relatively rare living groups such as horseshoe crabs and onychophorans that have not greatly changed.  Ancestral trees show relationships of major arthropod groups appearing rapidly during a few million years of time.

I do not have much hope of researchers finding fossils that clearly show the origins of annelids and mollusks more than indicated in earlier posts of this blog.  It is a little bit like me, not much is new since I turned ninety.

Joe Engemannn     Kalamazoo, Michigan     November 30, 2018

The issue from the mid-November Science issue had a bit about discovery of a method providing information about epithelial layers formerly thought to be unable to present fossil evidence.  It seems unlikely to provide reliable evidence leading to wholesale understanding of gross aspects of fossil structure, although interesting information seems to be revealed.

Arthropods ancestral to known groups may have not provided fossil evidence for a number of reasons such as - inaccessible ancient rock strata, lack of structures that fossilize,  Isolation of one or more small sub-populations of a species provides opportunities for more rapid development of new species.

My shutdown of blogging for the past month had nothing to do with the current government shutdown other than my wasting my time thinking about the ridiculous current events.

Joe Engemann    Kalamazoo, Michigan    January 7, 2019