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.

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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


Monday, July 16, 2018

THE MAJOR EVOLUTIONARY TRANSITION

Annelid worms are ancestral to all of the advanced major phyla.  Arthropods and mollusks retained annelid features as one major grouping of advanced phyla.  Chordates and echinoderms are the other major grouping.  The two groups share some common feature as a result of their annelid ancestries.

There are eight posts in this blog-site from 6/17/13 to 6/30/13 that are a more extended description of the basis for accepting the annelid theory of chordate origin.  The annelid theory eliminates the need to (1) assume a second early origin of segmentation and/or metamerism from acoelomate protostomes, (2) explain numerous bits of molecular similarity between coelomate protostomes and deuterostomes, (3) and, with the incorporation of information about the pogonophoran bottleneck connection provided in this blog, provides a logical rationale for the embryological differences as well as the mechanism of inversion of systems in the transition of protostomes to deuterostomes.

THE ANNELID PHASE

The pogonophora are fairly well established as close relatives of some marine polychaete annelids.  The fossil record provide very little evidence of events, but some annelid descendants clearly  existed during the pre-Cambrian.

Step one.  Tube-dwelling worms such as Sabella, started the rotation as they reoriented their posterior to a position in the sediments and left their plumose tentacles up in the water.

Step two.  Those becoming pogonophorans had multiple changes selected by the rigor of life at constantly increasing depths as they struggled to survive asteroid bombardments in the pre-Cambrian.  In particular, low metabolic rates due to abyssal pressure and temperature, tubes extending deep into the sediments for absorption of fossil nutrients, as well as retention of a blood vascular system to transfer oxygen from the water to the embedded end of the worm deep in the sediments, and loss a many non-essential features.  The thinning of the eggshell enabled dropping the spiral development of annelids and the ability of eggs to develop even if some cells were lost.  Loss of obvious segmentation left only a remnant of segments at the  posterior to anchor the worm in its tube.

Part  of step two was the reduction of the digestive system, particularly the mouth and esophagus.  This allowed the later fusion of the ganglia of the head into a brain blocking the mouth formation on the old ventral side.

Step three.  As asteroid caused extinctions in the surface areas of the oceans eased, progeny of the abyssal worms survived as they moved into shallow water and benefited by mouths developing where gut remnants touched epidermis on  the old dorsal side.  As they extending from their tube they now would use their relocated mouth to feed on particulate matter in their vicinity.

Step four.  As they increased their activities they were doing it with the old dorsal side now the new ventral side.  SO THE WORMS DID NOT ROLL OVER, THEY DID A BACK-FLIP as they made their transition from annelid to pre-Chordate organisms during the pre-Cambrian.

Referring to the February 27, 2015 post on "Evolution: the body cavity" may help you understand the bit about relocation of the mouth above.  The March 2, 2015 post on "Abandoned theories and Libbie Hyman"  has a brief discussion of the annelid theory and an associated figure.

THE IMPORTANCE OF THE REGRESSIVE  POGONOPHORAN STEP

The loss of features as pogonophorans adapted to life in the deep sea were essential factors enabling the climb to the branch of the animal kingdom known as the deuterostomes, with the vertebrates members dominating life on earth.  It enabled rearrangement of the head with fusion of ganglia into a brain and mouth formation on the former dorsal surface, simplified embryology of radial cleavage and delayed determination of first cells of the embryo.  The loss of ability to form chitin in deuterostomes meant other structural materials became more important.  Hemoglobin is the only blood pigment surviving in deuterostomes although a diversity of blood pigments are found in annelids prior to the pogonophorans.

OTHER PHYLA

There are other major and minor animal groups that are side shoots at many positions along the groups of the tree of life leading to as well as following the significant deuterostome branch.  They continued, some becoming extinct, others diversifying into forms still present.  One major group of arthropods, the trilobites, dominated paleozoic seas before becoming extinct.  The sponges of today no longer include the group giving rise to early protostomes.



The above figure shows the central sequence of protostomes leading to annelids from which all above them trace their ancestry and have coelomate body cavities.  The sequence follows a time sequence of origin of groups having living representatives (except for the hypothetical protonemerteans).  The pogonophorans provide a transition from coelomate protostomes to the vertebrate line that clarifies the transition without the mystery of many unknown ancestral groups coming from flatworms.

Many invertebrate groups such as ctenophorans, chaetognathans, lophophorates, echinoderms, sipunculids, extinct groups, and many others are not represented in the diagram.

Joseph Engemann   Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan      July 16, 2018

Thursday, May 10, 2018

EVOLUTION: AGING

AGING

Some animals have a programmed life of growth, reproduction, and death; mayflies and salmon provide commonly known examples.  Others seem to continue indefinite slow growth after reaching reproductive maturity, crocodiles, some fish, and lobsters are examples.  Warm blooded vertebrates generally cease growth when sexually mature because the growth zones of bones have turned into bone, so growth is limited to adding bulk - something not needed to get through the seasons of reduced food supply now that modern food production and distribution has arrived.

How I Got Interested In The Physiology Of Aging

Along with the natural interest we have about our own life expectancy, I got a boost in my interest during my doctoral research comparing two species of isopods with greatly different life cycles.  The ecological factors and adaptive strategies were understandable in explaining the differences.

Less than ten years later I was involved in incorporating new information about the pogonophora in a textbook revision.  As mentioned in the previous post about Ocean Circulation, the abyssal ones had life cycles several orders of magnitude longer than terrestrial and shallow water organisms.  The most likely cause was an extreme deep-sea pressure affect not likely to be a factor for air-breathing organisms.

WHAT HAS HAPPENED

A lot has happened to about double the global average life expectancy of new-born babies in the last century.  Probably the greatest factors have been modern medicine, disease control, care of newborns, care of mothers.  Popular papers, magazines, and other sources of health information have been filled with information, much of it worth your time.  There does not appear to be a secret food, exercise, or supplement that will answer all your health needs  A balanced diet with portion control, reasonable activity, and physician recommended additions may be best in conjunction with.

No smoking
     avoids many cancers, emphysema, intolerant non-smokers, and stress on the heart

No, or very moderate alcoholic beverage drinking
     may help us avoid cirrhosis of the liver, deposition of excess abdominal fat, falls, accidents, and DUI citations, need to take vitamins and minerals to replace ones missed by less intake of fruits and vegetables

Moderation
     in activities and intake of sugars, protein, saturated fat, and total calories - all are better than too much or not enough

Social life, sleep, and mental activity
     yes, and you will probably be happier with your extra years

Pick your parents
      too late, it doesn't matter as much as our environment.  Superb genes will not help if we engage in unnecessary dangerous activity or ignore safety precautions.  But don't lament your poor genes, passing on good behavior can be a factor more important in survival of offspring.

STROKES AND HEART ATTACKS

and the mental deterioration we often think comes with old age may be minimized by healthy living and a love for one another.  We can be in great health with only minor accumulations of cholesterol induced deposits in blood vessels, but a sudden episode of extreme exertion could cause a few clumps in blood vessels to break free and plug blood flow to areas of the brain or heart,  If it hits an unused part of the brain it may be no problem.  If it is small enough it may be only a short term minor problem.  But don't take the chance if you have been long retired from vigorous activity.  Take a smaller shovel full of snow, or don't try to keep up with speedsters; pause and enjoy the beauty of the day, and thank God that there was a time when you could do that.

OTHER POSSIBLE AGING FACTORS

Amino acids are predominately bent in the "l" form and may over time be gradually converted to the "d" form giving rise to no, reduced, or different functionality.  The process is probably gradual but may speed up due to radiation or other factors.

Telomeres that terminate the chromosomes may be reduced each cell division and reduce cell replacement in aging organisms.

Accumulation of waste, or other, products in the cells may reduce or eliminate cell function.  Some organisms such as some bryozoans may dedicate scattered polyps of the colony as storage sites of waste.  We can't do that.  But our kidneys do their best to maintain chemical balance in the blood and eliminate many wastes.  However some pollutants and toxic substances accumulate over time and are poorly eliminated.

Fat soluble contaminants accumulate in body fat as well as the insulating layer of some nerve cell processes of nerves and the brain.  Metallic elements may be retained by combining with body proteins.  The cumulative effect of such things may be intensified by weight loss from disease or dieting.  Impairment of function of organisms can result from injury and scar tissue.

Evolution and grandparents

Multi-generational families are almost a thing of the past.  But they were important in our evolutionary history by
    providing child care for young during our long childhood
    transferring information prior to written and electronic storage and transfer
    source of knowledge and wisdom aiding survival
    being the weak prey picked off by predators so others escape
    monitoring and alerting

Considering genetic values that might not seem to have selective value until well after reproduction has ceased, such as factors that contribute to post-reproductive longevity, natural selection would still be effective.  The genes that may not become active until late in life would be expected to be favored by natural selection as they are almost certain to be more abundant in the reproducing offspring of the ones having genes favorable to aging.  It involves the same principle of group selection enabling sterile worker castes of insect to evolve features beneficial to the colony but only expressed in the sterile caste.

The rapid evolution of increased brain size in humans can probably be accounted for by the benefits of greater memory capacity.  Large brains of whales and elephants, although not disproportionately large as compared to humans, have a value for retention of migration histories and social behaviors beneficial to the groups survival.

Joseph Engemann    Emeritus Professor of Biology, Western Michigan University, Kalamazoo, Michigan      May 10, 2018