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 -
https://evolutioninsights.blogspot.com/2014/06/the-baleen-whale-tooth.html

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

Monday, January 7, 2019

THE EARLY CAMBRIAN SPECIES EXPLOSION

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

Tuesday, October 2, 2018

Science: Understanding Statistics

Numbers

Numbers are meaningless by themselves for people that are not studying arithmetic or a related subject.  But we can all compare numbers and determine if one is bigger or smaller.  There is an old caution about people using numbers that notes "figure don't lie, but liars can figure."  Dr. Clark, teaching a biostatistics class, and later a member of my doctoral committee was comfortable telling an old joke about the statistician that drowned crossing a stream that averaged one foot deep.  I am currently puzzled by how I would know how many beers before I would sleep or blackout.  I haven't had a beer in over thirty years, and I found out over thirty years before that, that four was too many for me in one evening.  I seldom drink now, just an occasional small glass of wine or a drink traditionally garnished with olives, although I much prefer a glass of water.

Divorce rates

Our local paper has a front page story today, October 2, 2018, having the largest and first title "Millennials are causing the U.S. divorce rate to plummet".  The author of the article credits an analysis by a sociology professor using "U. S. Census Bureau survey data.  Others are cited who note boomers had married earlier and had a higher divorce rate.  Other factors are discussed that show how commitment and employment opportunities for women may be reflected in the numbers.

Toxic substances

Newspapers, magazines, and news programs are full of frightful stories about contamination or dangers of our food, water, medicines, and environment.  You are right to be concerned, and something should be done, but realize presence of some dangerous substances can be determined to number of parts per trillion (ppt).  Back fifty+ years ago, when I was a member of the Midwest Benthological Society and a graduate student studying bottom dwelling aquatic organisms and water pollution, few substances could be identified at concentrations less than one part per million,

Exposure limits

When tests associate the lowest level at which damage to test organisms is shown, permissible levels were typically set by regulatory agencies at one percent of the lowest exposure which produced problems.  Consideration should be given to other factors such as is it accumulated in tissues of an organism, is it persistent or does it break down naturally, how it interacts with other substances, and is it degraded or converted into other substances of concern.

 An extreme example

In the early 1960's when I was teaching at Western, I was prepared to testify at hearings for the planned Palisades Nuclear Power plant regarding their proposal to release very slight concentrations of radioactive elements in the expected cooling water releases into Lake Michigan.  Zero release was part of the final plan.  The seemingly small amounts had some elements that previous research (by others) had been shown to be concentrated by 30,000 times over the concentration in which they lived.  Take that concentration and note how they might be fed upon and concentrated in the food chain, or get filtered out an the beach, and the possibilities are frightening.  Fortunately, no releases were permitted.

In most cases, one part per trillion (a million of them to make one part per million) is not of itself a big danger.  But it does mean it might be coming from a more dangerous source that should be identified.

Food labels

Helpful, but ingredient lists can be more misleading than percent daily values.  Your jam or jelly may list a fruit first showing it is the most abundant food in the product.  But when you add up the later listed sugar, fructose, glucose, honey, and water, it would be possible that less than 20% is fruit and over half could be some form of sugar.  And if you are diabetic, you know the sugar content of fruit  eaten may increase blood sugar more rapidly than the sugars released by digestion of carbohydrates, thus drinking some orange juice is more apt to rapidly restore blood sugar levels reduced by a moderate overdose of insulin (this is not medical advice, just an aide to understanding an aspect of biology, consult your physician).  For more on glucose see the April 25, 2014 post "Evolution of Carbohydrates".

Joseph Engemann,  Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan    October 2, 2018

















































Friday, September 28, 2018

GLOBAL WARMING

Those of us living in temperate climates have winters and summers that clearly tell us weather can be cyclical, even dependably so when orbits around the sun bring recurring variations.  Less certain variations can add to or reduce the annual weather patterns.  A book that helped me understand more of how those variations impact our climate was published in 2009.  The author is perhaps the best informed climate scientist and deserves getting his message spread.

Storms of My Grandchildren by James Hansen (2009, Bloomberg USA, New York, 303 pages) notes on page xv of the preface that "Global warming does increase the intensity of droughts and heat waves, and thus the area of forest fires.  However, because a warmer atmosphere holds more water vapor, global warming must increase the other extreme of the hydrologic cycle--meaning heavier rains, more extreme floods, and more intense storms driven by latent heat, including thunderstorms, tornadoes, and tropical storms."

He had given related testimony to a Senate committee in 1988.  His earlier 1981 paper in Science "described likely climate effects of fossil fuel use".  And apparently was why "the Department of Energy reversed a decision to fund my research, specifically citing criticism of that paper as being alarmist."

The book makes one realize that money and politics inordinately influenced policy decisions beyond rational levels in the past as they do today.  Pages 124-139 added to my understanding of that.

I have had a few recent posts telling some of how the oceans have influenced evolution by their layered structure.  Hansen, on page 101, says "If we can measure how much the oceans are warming, we will know not only how much additional global warming is in the pipeline but also how much we must reduce the human-made forcing if we want to stabilize climate."

If you want to know more he has some good suggestions and explanations.  The most significant new one to me was the safety and efficiency of fourth generation nuclear energy which could operate safely using up the nuclear waste our first generation nuclear plants have generated (about 6 pages beginning on page 194 of chapter nine).

The solution isn't simple, the causes of global warming interact in sometimes uncertain ways.  But knowing about greenhouse gases, volcanic eruptions, fossil fuels, alternative energy sources, the sensitivity of glaciers, coral reefs, low-lying coastal regions, and the oceans might help us come to some partial solutions for saving ourselves and the biological world we depend upon.

Joseph Engemann,   Kalamazoo, Michigan   September 28, 2018

My thanks to Dr. Charles Heller for the loan of Hansen's book.

Thursday, August 30, 2018

Scientific Fraud

This month fraud was exposed, in numerous papers by Yoshihiro Sato, regarding clinical studies of supplements showing outstanding results in preventing skeletal fractures and/or other problems in elderly patients.  The dedicated work of Alison Avenell and Mark Bollard  was a major contribution toward exposing the fraud and subsequent retraction of many of the flawed studies.

Kai Kupferschmidt (2018, Tide of Lies.  Science, 361:636-641) doe a good job of reporting the results of their efforts and the difficulty of getting scientific and/or medical journals to address the issue.  The delays helped proliferate grants, studies, and publications that would never have been undertaken without the fraud.  The principle author committed suicide; co-authors often had no knowledge of the fraud and very small, if any, role in the research.

Their problems of dealing with publishers of fraudulent papers made me change my mind about trying to get retractions of two papers giving invalid support to Ecdysozoa and Lophotrochozoa as legitimate animal groups.  The authors did good work and were not fraudulent.  They were just mistaken in relying on other papers to support some poor scientific choices.

evolutioninsights.blogspot.com/2013/05/science-screw-up-no-1.html

The above address is for my sixth blog post on May 31 of 2013.  The errors in the criticized papers have probably been a major reason my views on the pogonophorans have gotten so little, if any, attention.  I just checked and the sixth post noted has had 15 page views.  The most popular post on this blog, about the body cavity, has had over 3930 page views since it was written in early 2015.

I was recently, in the process of trying to minimize the debris my heirs will have to deal with after I am gone, going through some accumulations packed before this blog was started.  I found numerous science journal articles supporting points I was trying to make in blogs I have written.  I have been writing mostly from memory and manuscripts I have written and research literature from reference files on my computer.  I should blog about some of those items before I get back to the clean-up tasks.

To the kind person who commented on my October 2015 "insect speciation" post (51 page views), thank you, you made my day.

Joseph G. Engemann    Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan       August 30, 2018.


Saturday, August 25, 2018

Book of the Decade

Lightman, Alan. 2018.  Searching for Stars on an Island in Maine,  New York.  Pantheon Books.  226 pages.

Delightful reading, perhaps a surprise for essays from a theoretical physicist.  He seems to be trying to reconcile truths of science and the humanities, which he now teaches at MIT, in twenty well written and understandable essays.

A French cave painting from 17,000 BC provoked thinking about humans and their role in nature.

Reconciling cause and effect leads to thoughts about our inability to prove absolute truth.  Absolute truths are most often claimed in theology (and the humanities?).  Some philosophers of science claim falsifiability is a requirement for for all scientific concepts, laws, and theories.  That does not mean they will be falsified, just that they must be capable of being tested by new hypotheses and evidence.

His fascinating blend of science and humanities topics, from the universe to subatomic particles, from the origin of the living world to the future of humans, will enlighten and hold the attention of most of us.

----------

He finds the evolution of our species, Homo sapiens, is likely to lead to Homo techno, a blend  of biological and electronic parts.  I personally think it is impossible to the degree he describes, but I was wrong about us never reaching the moon.

His search (for God and/or absolute truth?) described in his exploration of Jewish, Christian, and Islamic views, as well as a ten-day Buddhist retreat in Wisconsin, and discussion of many other views, and bits from classics in the humanities, is a marvelous story well worth reading.  But his scientific skepticism and application of humanities based thought leads him to a god much like mother nature.

I really like Alan Lightman, just from reading his book.  It would be great to sit around the coffee table discussing all sorts of things with him.  But, unfortunately, I can not sucessfully introduce him to God; he is still trying to use his skills as a scientist in the material world to prove God's existence. 

All he needs to do is ask God directly, God is everywhere and always listening.  He does not need to be knocked off his mount as St. Paul was, St. Paul already believed in God and was trying to serve Him in his way.

Joseph Engemann      Kalamazoo, Michigan     August 25, 2018

Friday, July 27, 2018

STEPS TO A REMARKABLE EVOLUTIONARY DISCOVERY

Discovery of the extreme age of the likely longest-lived animals on this planet was a slow process over many years.  It involved the combination of many discoveries by others that has not yet been comprehended by my peers, many of whom are much smarter than I am.  That the animals, the Pogonophora, are also closest living relatives of the link where the change from one major branch of the animal kingdom, the protostomes, gave rise to the other major branch of the animal kingdom, the deuterostomes, becomes understandable and obvious when all the facts are considered.

Getting ready for the discovery.

My early dreams as a biologist were to focus on some obscure invertebrate, that no one was interested in, so I could be the world's expert on an organism.  I didn't intentionally pursue that goal in graduate school, although I realized that many important discoveries had been made by people who were not looking for their discovery.

My master's degree research was about colony growth rates of a protozoan and its lipid cytochemistry as related to culture pH.  For that, Dr. Richard Fennel was my advisor at Michigan State University.

I began doctoral research at The University of Tasmania with the aid of a U.S.  Fulbright Scholarship to Australia in 1956.  A planned study of river pollution as indicated by invertebrates of the Derwent River was abandoned as impractical.  The chair of the zoology department there, Dr. Vernon V. Hickman, suggested a poorly known isopod crustacean living in pools on top of Mount Wellington as a good object of study.  It was.  Dr, Eric Guiler became my mentor for the isopod study while I was at the University of Tasmania.

Dr. T.  W. Porter became the chair of my doctoral committe at Michigan State University.  On my return, the committee thought I should enlarge on the comparative studies of the Tasmanian isopod with a somewhat ecologically equivalent Michigan isopod.  Both lived in temporary ponds approximately the same distance from the equator.

The isopod study provided background for understanding principles related to adaptive changes, early embryological development and extremes of life cycle length associated with anatomy, physiology, and environment.  I had no premonition that I would find it was preparation for recognizing important elements of the life cycle extremes, anatomical, and embryological adaptations of an organism with such evolutionary importance as the Pogonophora.  At the time I, like most biologists, had not even heard of the Pogonophora.

 Developing an interest in Pogonophora.


The interest came gradually as I taught invertebrate zoology and found out about the new minor group of worms, the Pogonophora, having no mouth and no agreement on how they took in nutrients.  The experts asserted that they were minor, degenerate, dead end, tube-dwellers of no evolutionary importance.  I found them interesting for having so many rings on their tubes, a possible indication of greater than usual age.  Most species were found at great depth, embedded in the ocean bottom.

Western Michigan University was the host of the C. C. Adam's collection of books and journal papers collected by the early ecologist.  The C. C. Adams Center published a series of ecology papers and used the publication in exchange for other publications.  One was Sarsia, a Scandinavian publication I might never have otherwise encountered.  M. Webb had several research reports in the 1960's; in 1964, two of special significance were published.  The first, described a rarely recovered rear portion of the worm with annelid like segmentation and setae.  The second, described a clear section of tube around the worm where it had broken through and secreted fresh tube.  It was similar to the upper portion of the same tube and indicated the tube was stationary in the sediment.

Webb's above findings sent me back to studies of marine sediments that show abyssal sediments accumulate very slowly,  The probable near vertical orientation of tubes and stable positioning, their length, and widespread distribution in the abyssal oceans where sediment accumulation rates are often extremely slow supported a conclusion that the worms reached great age.  Cold temperatures and low food supply seemed to support the idea of very slow growth when I put a question mark at the end of the title in a short paper, "Pogonophora: the oldest living animals?" published in 1968.

Studies suggesting verification of extreme age of pogonophorans.

Multiple studies found various indications of probable slow metabolism in the deep sea.  One of the most dramatic was the very low rate of bacterial metabolism indicated by the excellent condition of food after eight months in the submarine "Alvin" before  its recovery related by Jannasch et al. in 1971.

A recent post about ocean circulation showing the thousands of year needed for polar water to reach the surface indicates very slow respiratory rates in the deep sea.  It is more dramatic when you see many locations have high numbers of brittle stars in the photos illustrating Heezen and Hollister's 1971 book, The Face of the Deep.

Questions about nutrition of pogonophorans make the absorption of nutrients from pore water in the sediments a likely answer since Southward and Southward (1982) have shown that they can absorb nutrients from water where the concentration is as low as that found in deep sea sediments.

Studies suggesting the pogonophorans are the missing link.

I am embarrassed that I was so slow to see the pogonophorans as the link between protostomes and deuterostomes.  I was quite content with the posterior segmented body section discovered by Webb and the possession of chitin as reason for their polychaete ancestry.  The report of Gans and Northcutt in 1983 that developmental features of pogonohorans put them among the deuterostomes was unbelievable.  My distress was short-lived when I thought it was impossible unless they were an intermediate form; all the answers seemed to pop into my head- how that would explain the inversion, the changed embryology, and the hemichordate resemblance.

There are many more features of advanced protostomes and deuterostomes made understandable by common ancestry instead of convergent evolutionary origin,  The different evolution rates possible are also well illustrated by understanding the pogonophoran's evolutionary position.  My isopod study, teaching a broad range of biology courses, and having to write a new section on pogonophora, provided needed background for discovery of the important evolutionary role for the supposed evolutionary dead-end, the Pogonophora.


Joseph G. Engemann    Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan      July 27, 2018