Monday, June 30, 2014


God: Lection Divina


Lectio Divina is an approach to spiritual reading of the Bible.  The five components are described in a brief account by Stephen J. Binz in the July/August issue of the the WORD among us.  A 152 page book on the topic by the same author is also available from online.  It is an approach to scripture reading, not a method.

First, read, one reads or listens to the word of God in some passage of the Old or New Testament.  The blend of daily readings listed in the WORD among us can be a good starting point.  I have been doing that for perhaps a dozen years.  My early attempt to read the bible from cover to cover was never completed as I bogged down in the first few books.  Later, I found that opening the bible at random and sometimes looking up particular topics of interest was quite a satisfying source of inspiration.

The real key is realizing that it is all inspired by God although the historical accounts in the Old Testament often leave one wondering until it is understood as leading up to the New Testament of the life and teaching of Jesus Christ.  For example, the stern approach of the Ten Commandments becomes understandable when viewed by the two commandments of Jesus to love God and to love others as we love ourselves.  When we realize God's awesome grandeur and great love for each of us, how can we not but want to behave as the stern first three or four commandments require.  Similarly, if we see how much God loves each of us and wants good for us, how could we desire to treat them less lovingly, therefore we have no need to be reminded by the remaining commandments.

Second, meditate, think of the message or meaning of what you have read or heard.  Consider what message it might contain for you today.  Be relaxed as you reflect, expect God to inform you.  Often the same passage may give you different insights at different times as your needs change.  Reread parts as needed.  Footnotes and references to other passages may be profitable.  For example, a reading for July 1 from Matthew differs from Mark regarding who entered the boat first before the miracle of calming the sea.  The reaction of the apostles and the miracle are obviously the important messages.  Perhaps Matthew's source was following up the group and Mark's was near the front, probably a fact of no consequence.  Some passages may leave me puzzled.  Some were coded to avoid provoking civil authorities persecuting Christians; scripture commentaries may help in such cases if footnotes do not help.

Third, pray, respond to God with your thoughts of praise, of his goodness, of your repentance for misdeeds, your needs and needs of others you know.

Fourth, comtemplate quietly and relaxed awaiting God's message to you.

Fifth, proceed to apply what you have learned from the first four steps in your life.  It doesn't have to be a dramatic change, just keep at it.

I have a beautiful picture of the title page of the bible I been reading for the last twenty some years.  I decided not to include it because of copyright considerations, so look at yours.  Crack the book for me and read a passage that catches your eye.  Thanks.

Joseph G. Engemann    June 30, 2014

Monday, June 16, 2014



Current phylogenetic trees that include Ecdysozoa and, to a lesser extent, Lophotrochozoa are grossly incorrect.  Because DNA neucleotide sequences are subject to selection and have had different rates in different groups the direct calculation of rates from comparative differences produces flawed evoutionary trees.

This can be shown graphically by comparing two branches of a phylogeny using the different assumptions involved.  The determination of when and how fast the differences in longevity develop is subject to error also, but, in the case of the descendants of pogonophorans, may rapidly move to shorter life cycles as soon as the transition from abyssal to shallow depths occurs.  Thus very few new species may make the connection of ancient pogonophorans to those that became the earliest shallow water deuterostomes.

 The first figure illustrates two types of error made in calculating phylogenies, generation time error and calibration error.

Generation time error is the one that produces incorrect branching in a phylogeny.  The figures illustrate generation time error for two species assuming that half the change occurs in each line as in the 5 and 5 of the right figure of each pair.  When 90% of the change occurs in the right branch, the estimated time from origin at the ancestral node is nearly doubled.  With pogonophorans having generation times several thousands of years longer than modern non-abyssal species, the node where deuterostome phyla branched off is clearly during Pre-Cambrian times as is also suggested by the Paleozoic emergence of chordates.

Calibration error is one that can cause overestimates or underestimates in the time of divergence in two lines from the ancestral node.  The two right figures keep the generation time error intact, if it is in error.  The calibration error occurs when the time per nucleotide change is based on a calibration species whose rate of change is different from the species to which the rate is applied.  Selection of a calibration species or a rate of change is not likely to be a major problem when closely related species are studied.

If you think about the result of the generation time error introduced by the central position of pogonophorans in the protostome, deuterostome radiation, it is not surprising that their relatively unchanged DNA shows affinity with widely diverse phyla.

A similar problem is probably operating in the nematodes being a significant group in the erroneous group, Ecdysozoa.  The small size of nematodes is probably a selective reason nematodes have a single gene per gene family and thus a more rigid selection producing relatively unchanged genotypes over a long. time.  Thus the "long-branch attraction" is not recognized as the error compounded in the Ecdysozoa concept.

The last figure illustrates one possible view of the development of two species having different longevity from a common ancestor.  It is perhaps worthless as an illustration because the common ancestor of related species, one with a one year life cycle, the other with a two year life cycle, could very well have resulted from all the change in one line, or both from greater change from some extreme value.  Rates of change are also unlikely to be so uniform.

Until I stumbled across what seemed to be an unlikely ancestral role of the pogonophorans I would have been been very likely joining my peers in welcoming the Ecdysozoa and Lophotrochozoa.  I hope I have included enough information in the blogs on this site to help my peers make the same transition I have made.

Joseph G. Engemann      June 16, 2014

Friday, June 13, 2014



The pogonophorans almost certainly include the oldest living individuals among their numbers in abyssal locations.  Bacteria in salt crystals have survived for longer times in a relatively inactive state.  Corals and sponges as noted in my living fossils post of May 30, 2014 probably survive longer as colonial animals that have new growth cover old dying portions.  But the Pogonophora are the champions as evidenced by their tubes in ancient sediments and their molecular relationship to other groups only likely by the fact that they are relatively unchanged from the ancestors of diverse groups.

Evidence from their tubes

If the tubes are vertically positioned in the sediment, the age of the sediment at O (origin of tube) in the diagram above would indicate its age.  If the rate of deposition of sediment is known, D, (the depth) of S (surface) to O can be used to calculate age.

The tubes of many species of pognonophorans are very long and slender.  They may be less than a millimeter in diameter and as much as a meter long.  Many of them are at abyssal depths where sediments accumulate at a rate as slow as 1 mm. per 250 years (a rate noted by Ekman, 1953) for deep sea sediments.  Among faster rates receiving more abundant sediment nearer continental margins, a rate of 3 cm. per 1,000 years (rate from Ericson et al., 1963) is at the other end of the range of likely rates lacking exceptional fast deposition.

If the banded portion of the tube was 30 cm deep in the faster accumulating sediments it would indicate an age of (30/3 x 1000), or 10,000 years.  If it was 50 centimeters deep in the slowest accumulating sediments it would indicate an age of (50 x 10 x 250), or 125,000 years.  These are probably conservative estimates because length of tubes may be much greater as indicated by the posterior end of the worm (as discovered for Siboglinum fiordidcum by M. Webb, 1963), has segmentation and setae, which is seldom recovered.

Only the banded portion of the tube indicates original depth because worms with a posterior that breaks
through the tube below are in a portion not banded as shown by illustrations of ones discovered by Webb.

Most tubes have some type of banding undoubtedly associated with growth, but the growth intervals are uncertain in the nearly uniform, almost unchanging seasonality of the deep sea.  Perhaps growth periods are related to the rate of accumulation of sediments or to growth between periods of reproductive stress.  That some have fluted growth rings indicates tubes are stationary in sediments.

Ivanov (1963) illustrates different species of pogonophoran's tubes, many of which have fluting as illustrated with regular or variable spacing.

As noted in the June 22, 2013 post, many features of abyssal depths contribute to slow or prolonged growth.  Physical factors directly slowing growth are constant near freezing temperatures and extreme pressure (perhaps by affecting rates of diffusion needed for life processes to proceed); the physical factor of absence of ultra-violet radiation would not slow growth but would aid survival.  Reduced competition and low predation, a low concentration of dissolved nutrients in the sediment, and K-selected extremes also contribute to survival and long life spans.

Other posts indicate support for the long life by the ancestral position intermediate between the more ancient protostome lineage and the more modern deuterostome lineage.  The vertical orientation is an intermediate condition needed to produce the inversion of systems noted by annelid chordate comparison.  The extreme longevity result in proportionately slower rates of genetic change so genetic similarity to all descendant groups is increased as compared to extremes compared within the new groups.  Failure to account for the various rates of evolution is the main source of phylogeny errors in current views of relationships of phyla.

Joseph G. Engemann     June 13, 2014

Monday, June 9, 2014



Michigan vs. Tasmanian isopod rates of evolution

The Michigan isopod (posted 6/5/2014) with the egg appendage was able to complete two generations per year.
The Tasmanian isopod  (posted 6/1/2014) took three years to complete a generation.

Since generation time is a reasonable measure of potential evolutionary rates, there is a six-fold difference in the potential rate of change from the ancestral type between the two groups.  Thus it is reasonable to expect the Tasmanian ones have greater similarity to the common ancestor of the two groups.  The greater change in the Michigan one was reflected in the flattening of the group, the fusion of abdominal segments of the upper surface of the exoskeleton, and the development of appendages on the egg; these changes do not appear to be evident in the mostly likely ancestral types of crustaceans.

Potential rates of change are just that, potential.  Selection may keep a well-adapted set of species characteristics relatively unchanged for a longer time than expected.  In such a case, molecular changes may occur in DNA sites not readily affected by selection and thus be a better gauge of time of separation from ancestral types than indicated by unchanged anatomical features.

In ten generations, if x were the numbers of nucleotide changes per generation, the Tasmanian one could have accumulated 10x number of changes and the Michigan one 60x number of changes.  Changes to 100% of the genome would take six times longer in the slowest, so more species could be expected to develop in one with a shorter generation time, if rate of potential change were the only operative factor.


Speciation, or development of new species, is usually thought to require geographic isolation from the ancestral type.  Species are sometimes defined as having reproductive isolation from each other.  Geographic isolation can make interbreeding impossible and has been a major factor in evolution.  But isopods having a three year generation could have three species going separate evolutionary paths in the same location.  I wondered if it may have been a factor in the presence of multiple species of similar isopods in Great Lake in the central highlands of Tasmania.  I was not able to determine that although Nicholls listed several species from Great Lake.

Cicadas, some species of which have 17-year life cycles, have developed identifiable differences in some different year-class broods found in the same location.  Speciation may have occurred in some invertebrates of the seashore based on different breeding times during the same year by selection differing at the beginning and end of the breeding season, along with higher predation on early life stages  by predators focused on the peak at the middle of the breeding season..

In addition to geographic and temporal isolation insects are spectacular in their diversity that is a result in part of rapidly gaining reproductive isolation due to specification of genetalia modifications often referred to as a "lock and key" arrangement.  As a result hybridization is prevented once genital differences are sufficient.  Insects may also be reproductively isolated by life on different- host plants or animals, or with pheromones, behavior, and microhabitat differences.


I wondered why such long generation time occurred in the Tasmanian isopods.  As a result I became sensitive to the causes of long generation time.  That followed me long after studying isopods.  I had concluded that the rapid input of much nutrients enabled Michigan isopods to specialize for rapid life cycle, with quick growth and the ability to produce many eggs to capitalize on the period of abundant food.  At the same time it enabled them to persist in the presence of high levels of predation.  So I was familiar with the biology of r- and K- selection before R. H. MacArthur and E. O. Wilson were first to write about it in such publications as their book, The Theory of Island Biogeography (1967).  Their elaboration was a valuable contribution to better understanding of the impact of ecology on evolution.

Long life, infrequent and delayed reproduction, low reproductive rates, low food supply, absence of or low predation and/or ways of avoiding predation, and slow development are all associated with K-selected extremes in the biology of a species.  Within the same habitat it is possible to have both extremes represented as in the example of the cicada with a dozen or more years needed to complete its life cycle while another heteropteran insect, the aphid, can have many generations per year.  Large size usually is accompanied by long generation time, but not always.


As a result of this interest in longevity, I was prepared in advance to recognize the extreme length of life of the pogonophorans.  Their slow evolution and ancestral role were also able to be seen due to that and the knowledge of invertebrates partially acquired by revising Hegner's Invertebrate Zoology text for its 1968 edition.  A continuing interest in animal evolution led me to recognize some of the errors infecting it now as shown in the post of May 31, 2013.

Joseph G. Engemann      June 9, 2014

Thursday, June 5, 2014



Baker Woodlot Vernal Pool, home of the isopod studied in Michigan

Baker Woodlot on the campus of Michigan State University in East Lansing, Michigan contained several vernal pools.  One by the road on the western boundary of the woodlot was the location where the population of the isopod, Asellus communis, studied for comparison was found.  As compared to the elevation of the pools on Mount Wellington of over 4,000 feet, the elevation is less than 800 feet.

                                  Vernal Pond in Baker Woodlot

The pools were almost equidistant north or south from the equator, but in opposite hemispheres.  The temperature extremes were not measured but the mild temperatures of Hobart at sea level were replaced a few miles away by colder temperatures on Mount Wellington, especially during the winter.  Trees provided an abundant leaf-fall in the woodlot.  Input of similar nutrients were much more limited on the mountain.  Vertebrate predators such as turtles, fish, salamanders, and frogs were not found on the mountain and are relatively few in number in Tasmania.  More species of invertebrates were found in the Michigan pool.


Both species had females with eggs in brood pouches during the breeding season as shown in the figure of Asellus above.  The difference between the 2nd and 3rd pleopod sizes of the Michigan isopods are shown in the drawing; pleopod 3 covers 4 and 5 on the underside of the very short abdomen (in above figure A).

The egg appendage

The photo A below shows two eggs.  All Asellus eggs develop pairs of egg appendages; one, B,  is enlarged for clarity.

The cells forming the tissue of the appendage have characteristics much like the leaf-like branches of the pleopods under the outer protective branch of the 3rd illustrated.  The delicate cellular structure indicated by B and its similarity to the respiratory appendages suggests the appendage has a respiratory function; the same features could be useful in eliminating ammonia and perhaps other water soluble wastes.  It has been suggested that they could be useful for uptake of nutrients from the mother's brood pouch.  That does not seem likely since water from the pool bathes the eggs, and the eggs have a plentiful store of nutrients in the darker yolk filling the egg.

The Tasmanian isopod eggs (upper left in figure above) do not have external appendages.  The Tasmanian isopods have many points indicating a closer relationship to ancestral crustaceans.  The Michigan ones, in addition to having the egg appendage, have dorso-ventral flattening and fusion of abdominal segments.  Fossil evidence suggests the antiquity of the Tasmanian variety.The egg appendage presence clearly illustrates that evolution can occur in developmental stages independent of adult evolution.  So the use of embryological features as evidence of relationships has to be done cautiously.  The appendage seems to have homology with a simple bulge (paired bulges, one indicated by central semicircle broken line) in the same position on the side of the folded embryo in the egg of the older group.  A peculiar fact is that the appendage sometimes persists briefly (at the point on the adult indicated by the arrow) on newly hatched isopods as illustrated in Sars' 19th century work on The Crustacea of Norway.  The bulge on the embryo of a South African species similar to the Tasmanian one persisted briefly after hatching in one studied by Barnard.


In summary, the egg appendage of some isopods is good evidence that the old biogenetic law - that the development of an individual repeats stages in the evolution of the group - was correctly abandoned. Adaptive features can develop in any stage of the life cycle independently from development of other features.  Although  the theory has been abandoned, the stages often do give clues to relationships when viewed in the proper context.

Joseph G. Engemann     June 5, 2014

Wednesday, June 4, 2014



The largest terrestrial isopod that I know of is from the same suborder of the one I studied in Tasmania.  But it is much bigger and is adapted to life in shallow tunnels beneath the ferns, eucalyptus trees, and other vegetation of the cloud forest of the Ottway Mountains in Victoria, Australia.

I was trying to visit and collect specimens of the sub-order to which the isopod on Mount Wellington belongs.  Nicholl's monograph on the Phreatoicoidea indicated the type locality from which the species (Phreatoicopsis terricola) had been collected was about 20 miles from where I left a bus the take the road in the picture.  There was no public transportation along the road leading to Beech Forest where a small map on a postcard indicated a railroad existed.  Halfway to Beech Forest the map showed the town Olangalah.

Before reaching Olangalah I thought I would check to see if maybe isopods would be in the rainforest pictured above. When I got down a short distance into it and dug with a trowel I found tunnels immediately about an inch deep.  They were perhaps an inch or two in diameter and contained the isopods shown below.  I had to be careful to keep my distance from the abundant fern fronds, many of which had terrestrial leeches perched on the fern tips and ready to attach for a meal of my blood.

The isopods had a little yellowish pigmentation on the head.  The transparent body revealed a gut full of what I assumed was organic rich soil.  I put some in a jar without much water but adequate airspace and they survived the trip back to Tasmania.  But along the way I had some difficulties.  When I got back on the road and came to an opening with empty fields, I was sure it had been Olangalah, I was relieved I only had a few more miles to go before I got to Beech Forest.  I think maybe one car had gone past me before I thought I should try to hitch a ride.  A couple more went by the wrong way before I got to Beech Forest.  I found a hotel where I could get something to eat and asked about the train schedule to Melbourne where I had my ticket for a flight to Hobart the next day.

The only train was a weekly one that wasn't due for a few more days.  So I started hiking along the road to Melbourne.  It was dark when I passed the location by the Beech River where I had been hoping to collect the isopods.  Attempts to hitch-hike had been unproductive, I'm sure I wouldn't have picked up a hiker as disreputably looking as I was with boots and knapsack.  So I continued along the road winding up the mountain from the river valley.  In the wee hours of the morning I lay down along the road to rest, there had been no traffic for a long time.  I aroused with some hope as I heard a vehicle in the distance.  After what seemed like at least twenty minutes a large truck pulling a trailer with an enormous eucalyptus log approached and stopped.  When I asked if he could drop me of anywhere I could get transportation to Melbourne, he told me he was going to Melbourne.  Wow, what relief.

The big terrestrial isopods are quite small compared to the largest known isopods that are found at great depths in the ocean.  Shedd Aquarium in Chicago had some (Bathynomous gigas) on display the last time I was there.  The marine isopod is in the suborder containing the pillbugs, or sowbugs, and the aquatic isopods of the Northern Hemisphere.

Joseph G. Engemann        June 4, 2014

Monday, June 2, 2014

The Baleen Whale Tooth


In a previous post I thought I had referred to discovery of a tooth on a baleen whale's nose, but the posts on whales of last August and September did not have it.  So, at the risk of being repetitious, a whale that had washed up on a Tasmanian beach about six months before the pictures below were taken, in 1956 or 1957, was badly decomposed in the part exposed to the air.  The part deep in the salt-water laden sand still had fresh-looking red whale meat.  It had been identified as a Pygmy Right Whale.  We were there to get as much of the skeleton for the University of Tasmania's collections as my advisor (Dr. Guiler from the Zoology Department), another faculty member from the university, and myself could.

The ribs in the foreground were pulled from part of the carcass after the layer of skin or blubber (the brown layer that also had not decomposed) was moved.  As is evident the very gently sloping beach was perhaps a factor in the whale beaching itself.  It probably lacked a reflective surface to effectively return signals to the whale telling of the end of the ocean.  The skull is not obvious in the photo, but in the photo below you can see the part of the jaw with the tooth at the end is already quite weathered by exposure.

The tooth is of interest for several reasons.  It is certainly an indication the whale is derived from a toothed ancestor.  Its persistence suggests it has had some survival value in its ancestors and probable continuing value.  It may be of value in ramming an opponent.  The saga a few years ago of a whale in danger of being trapped in the Arctic Ocean as early winter ice was forming made me think it might be of use in fracturing the ice to enable breathing to support it for a longer under ice trip to open water or a new thin area to break.  It might suggest a relationship with narwhals and their long tusk.

If you read my posts on creativity you should realize we should at least consider the possibility that the tooth is a new development rather than a holdover from ancestors with tooth filled mouths.  I think the fossil record is adequate to dismiss such an idea and go on to other things.  One of those things might be the observation that marine mammals are thought to be the only placental mammals native to Australian shores and lands other than the bats prior to the arrival of humans.  So I will end with an example of a bat from Tasmania, circa 1957.

Joseph G. Engemann     June 2, 2014

Sunday, June 1, 2014


Mount Wellington, home of the isopod studied in Tasmania

Isopods are common marine, freshwater, and terrestrial animals with seven pairs of legs.  The one most familiar to you is probably the one that rolls up in a ball when disturbed after you pick up your flower pot.  Most are flattened so top and bottom appear close together.  But the one in Tasmania is part of an extremely old group and does not have that flattening, in fact it appears as though it is flattened with the sides closer together.

Mount Wellington is a little over 4,000 feet tall.  The summit is only a few miles from downtown Hobart, as shown from the harbor on the Derwent River below.  Darwin had difficulty reaching the summit, which he did late in the day on his second try.  It was much easier for me because a road had been built to very close to the summit.  The back side of the mountain still has tree ferns as noted by Darwin in his Voyage of the Beagle along the Northwest Bay River which is fed by the mountain top pools.

The isopods on Mount Wellington and others in the same suborder are now restricted to the Southern Hemisphere.  Although first discovered in well water in New Zealand, most species are found in Tasmania, with only three in South Africa.  Their discovery came after Darwin's visit to Tasmania and Mount Wellington where he may have trod through the pools where they are found as he gazed out from the summit and saw the views below.

What looks like moss covered rock is really the dense growth of branches of a composite noted below.

The pools around the round green composite Abrotenella fosteroides in the first picture closeup were sampled periodically for a year.

This view from just beyond the pool containing the isopods shows Ralph's Bay and the Tasman Peninsula to the East of the summit lookout.

At least a three year life cycle from egg to isopod to egg

All the isopods in one kitchen strainer scoop were collected, counted, and measured.  During the Australian summer they were inactive in the dried but damp pools.  When pools refilled in the spring, a new batch of young were released from the brood pouch (formed from plates extending from basal segments of four pair of legs) for the annual crop of young.  A maximum of 19 young or eggs were counted in pouches from other samples.

If you notice carefully you can see two or three age classes in the November sample. In the May sample only two of the young from the previous date were included as the new young became quite numerous.   A possible middle group from November is merging with the adults.  Relatively few adults were found in the July sample, although in August they were abundant.  Part of the disparity of adult numbers was probably due to the fact that many females with eggs were abundant under the green composite shown, while my samples came from the flocculent sediment in the deeper part of the pool.

The pools were above the timber line on the mountain and had snow and ice part of the winter.  But it did not appear a factor in reducing the number of generations to one per year because a population of closely related isopods had the same growth pattern at sea-level on nearby Bruny Island.  Just for the record for interested zoologists, the isopod is Colubotelson thomsoni in the suborder Phreatoicoidea.  It is usually viewed from the side because the flattening make a specimen lay in that position as in the photo above and the figure below.

The pleopods beat in a channel made by downward projections of the sides of the abdominal plate.  They are the respiratory organs of the isopod, although in the male a portion of the second one is modified for sperm transfer.  This region of the abdomen retains the segmented nature whereas in the Michigan isopod (Asellus) the segments of the exoskeleton are fused.  Because of the flattening, its pleopods are exposed and the third one has a protective plate shielding the ones behind it.  The first two, unprotected are greatly reduced but the sperm transfer appendage of the male is still functional.  So both sexes have the respiratory function of the first two pleopods lost by selection driven by the selective value of the arrangement for the male.

The eggs of the Tasmanian isopod have about twice the diameter of the Michigan ones.  The egg shell is also about twice as thick.  Development to hatching takes several months in contrast to about two weeks for the Michigan one.  In a upcoming post I expect to show the egg appendage of the Michigan one which may help in its speedy development.

Joseph G. Engemann      June 1, 2014