EVOLUTION, SCIENCE AND EXTRATERRESTRIAL LIFE

Evolution, Science, and Extraterrestrial Life

EXTRATERRESTRIAL LIFE

The search for extraterrestrial life was featured in a NOVA, or some other, television program I happened across yesterday.  Over the years I have come to the conclusion that there are people on countless other planets in the universe, but that documenting or proving it is impossible.  Still, it is worth considering the arguments and evidence that might convince us of the existence of someone with a potential to communicate with us from some far galaxy.

SCIENCE

The most hopeful search described on television was an attempt to detect radio-wave transmissions from outer space via a reception on a radio-telescope array.  Radio-waves are presumably subject to no, or less, distortion as they travel through space and matter intervening in space.  The opportunity for success is infinitesimal, or so close to zero, that I doubt it is worth the effort for the following reasons.

1.  Pinpointing a source would be more difficult than spotting an ant on earth from a telescope on the moon.

2.  A potential source would likely be of short duration relative to the long time the signal would take to reach the earth.  Possible reception from pointing the radio-telescope at the right planet or star might also precede or follow the time a signal is generated.

3.  The algorithms and signals that brilliant minds are expected to develop and send my never be sent because they are even more intelligent and understand its impossibilities or lack of potential use for communication requiring many years between sending and receiving.

4.  The formation of galaxies, stars, planets, and the elements likely to produce a potential life inhabited planet happened many millions of time during the development of the universe.  But those millions are too isolated by time and space for even a slight chance of discovery.

EVOLUTION

Of the many billions of planets produced, millions have likely gone through an evolution of carbon-based life that could well have produced conditions needed for the evolution of life during some period in the past ten billion years.  It would have required several things.

1. The right blend of chemistry, temperature, radiation, gravity, and relative stability of conditions.

2. Sufficient time with those conditions.

The natural selection outcomes would result in evolution likely including some outcomes with

1. Biochemical features much as organisms on earth have.

2. A lot of systems similarity to earthly organisms.

3. Similar ecological roles for different groups of organisms.

4. Social structure, and greatest technological advance with an organism about the size of humans, probably bipedal; but perhaps with different numbers of digits and vertebrae.  They would probably dream about being able to fly like the little fliers and the big fliers of their worlds.

A big question, would the dominant organisms have pigment variations like us or would they all be green?

CREATIVITY

Silicon based versus carbon based life systems seem an interesting possibility in science fiction.

Some find the interacting whole of the biosphere is some type of organism; there are interesting parallels between biosphere and organism that are better explained by ecological principles.

GOD

God is probably amused by those people on planets to whom he* was willing to reveal himself* for their belief that they are the only ones of importance to him*.

* I don't think God has a struggle with our inability to come up with an agreed upon, non-gender based way of describing I AM. I AM, the creator of the universe and all that is in it as well as the underlying or embedded principles leading to the world and its ways.

Conclusion: extraterrestrial life probably exits in the present, probably existed in the past, and will probably exist in new places in the future.  We are unlikely to ever know for certain from physical evidence in our present state.


Joseph G. Engemann    Kalamazoo, Michigan    October 4, 2014

EVOLUTION: NUCLEOTIDE MUTATION RATES

Evolution: Nucleotide Mutation Rates

MOLECULAR CLOCKS

If nucleotide mutation rates were the same for all organism and all parts of the genome, they would be the basis for a perfect molecular clock to determine relationships for constructing evolutionary trees.  But they are neither the same for all organisms nor even for various portions of the genome for the same organism.

For those wishing a more comprehensive view of the variables, they may be found by searching for nucleotide mutation rates in Wikipedia, or elsewhere, on the internet.  To the best of my knowledge, my peers have neither found nor embraced the evidence I have presented in other posts on this blog showing the major errors in the current published articles on the relationships of phyla and the importance of the Pogonophora in demonstrating those relationships.

MUTATON RATE VARIABLES

Some variables are known but not considered in several major studies, thus producing major errors in proposed schemes of animal evolution.  A variation produced by different generation times is the major factor affecting rates of origin of phyla when extremely low evolutionary rates occur - as noted elsewhere in this blog for pogonophorans and perhaps nematodes.  Most variables would have a proportional affect within the variation caused by generation time.  Fortunately, the affect of generation time diminishes to near zero as one approaches the species level.

Variables

There are many documented studies showing different rates for different groups of species.

1. Viruses with RNA genomes mutate at a much faster rate than organisms with DNA genomes.

2. Mitochondrial DNA has a faster mutation rate than nuclear DNA.

3. Methylated DNA is more resistant to mutation than DNA that is not methylated, as in sperm which have higher mutation rates than eggs.  This is perhaps tied in with the fact that sperm genes may be expressed in the individual produced more than is expressed by genes from the egg.  Methylated DNA from the egg may also be a reason that dosage affect on gene expression has less impact than one might expect from comparison with instances where three of a particular chromosome are present.  The methylation effect is not total; that is shown by Medel's pea experiments where the flower pigment expressed is dosage dependent, and in humans where the sickle cell gene is less debilitating in the heterozygous condition.

4. Mutations are more likely to occur near sites where chromosomal deletion or insertions have occurred than in more distant locations from those mutated sites on the chromosome.

5. Genetic factors may affect rates; perhaps through variations in function of chromosomal damage repair functions.  Rates may be subject to natural selection balancing the value of introducing change versus the stability desired in successful genes.

6. Environmental factors such as variation in background radiation and/or the extremes of deep sea pressure  may also affect rates.

7. Generation time is the current source of error in relating major groupings of phyla.  This error is also a factor in proposals of a time of origin of humans relative to monkeys and great apes.  But it is not a factor in most studies of animals sharing the same species, genus, or family.  However it may be more of a factor as one compares orders and classes of animals.

A botanist colleague maintains generation time is not a factor in evolution of flowering plants, although I think that has yet to be proven.

Generation time versus age affects?

The question might be of interest in human evolution because older individuals may be more likely to have experienced mutations in germ cells, especially sperm, whereas eggs may be spared much of the generation time effect by all being produced before birth as well as by having methylated DNA.

I have not given much thought to this as a general factor because it does not seem apparent for animals in the deep sea that were critical in providing the clue of the annelid ancestry of chordates.  If long generation time corresponds with more mutations per individual, it would seem to cancel out to some extent the generation time effect in evolutionary rates.  The extreme difference of generation time of abyssal animals critical in the early origin of phyla makes cancellation of this type of little importance when considering overall evolutionary trees of the major groups of animals.

Natural selection

The rate of mutations may not have as much to do with evolution as does natural selection.  Beneficial mutations, although they are much rarer than other mutations, tend to be incorporated in the species gene pool via natural selection or survival and reproduction of the individuals having them.  Whereas deleterious mutations tend to be eliminated.  In mammalian species much of the genome is thought to be non-coding and in the regions of the chromosome between the genes or coding regions.  Mutations in the non-coding regions are thought to be of little consequence as long as they maintain the chromosomal integrity.

Although rates are not necessarily of major impact on the direction of evolution, they are essential to consider in establishing the branching pattern of evolutionary trees, especially as regard major group relationships.


Joseph G. Engemann    Emeritus professor of Biological Sciences, Western Michigan University  October 1, 2014

SCIENCE

Science: Data Selection

DATA SELECTION

Scientists view data selection as forbidden.  That is certainly appropriate in a well-designed study if everything goes smoothly.  But it seems appropriate to exclude data that results from defective instrumentation, obvious errors in recording data, and inclusion of data not meant to be part of a class being compared.  Any departures from selecting data after it has been collected should be included in notes of research reports.  Even the best of intentions of researchers can sometimes result in compromised data that should never have reached publication after good peer review.  Some examples I have encountered follow.

Salamander growth 

An excellent field study done by a former colleague showed a continuously rising straight-line growth curve.  My familiarity with growth curves from investigating the principle of growth pertinent to my study of protozoans during my master's research project and crustacean growth in my doctoral research made me dubious about the salamander growth reported for the Central American salamanders.  Dr. Vial informed me that his doctoral committee had approved excluding some data thought to be defective in the study.

I was discussing his study with him after a seminar he presented about it.  Successive years data from salamanders that had not grown were excluded for fear that they were not from the same salamanders but were ones that had lost toes that made them misidentified as ones from his toe-clipped sample.  I don't remember for certain if they were also excluded for possibly not showing any growth due to tail loss and incomplete regeneration of a new tail.

It is likely that his salamanders growth slowed with age due to one or more of the many factors that can slow growth.  The rapid growth of young individuals slows and in many species stops before natural death occurs.
1. Energy put into growth diminishes as more energy is put in to reproduction.  2. Increased size may not be accompanied by an accompanying supply of materials for growth.  3. Accumulation of waste within cells may slow growth.  4.  Conversion of l-isomers of amino acids to d-isomers may interfere with metabolism.  5. Telomeres of the chromosomes may be reduced beyond numbers needed for growth.  And, 6.  Genetic control causing growth cessation may have evolved through natural selection to keep the species age class composition supplied with young and vibrant individuals.  Regions where such populations occurred would likely replace adjacent populations not doing so.

Remote sensing

Another colleague made the assumption that remote sensing of lake colors by satellite could measure lake quality.  The assumption was correct in a general way but I knew of one specific case where it did not work as planned.  Asylum Lake was one I frequently sampled with my aquatic ecology (limnology) classes.  Years of food wastes had polluted it severely although recovery was proceeding after it stopped.

During the years of his study I had noticed the surface often had many floating bits of duckweed, one of the smallest aquatic green plants.  Their chlorophyll is of a type associated with green algae that are found in lakes not severely polluted.  The algae suspended in water beneath the surface were primarily blue-green algae which are indicative of lakes over-enriched with phosphorus.  So the lake by that assessment was eutrophic and not oligotrophic as the remote sensing indicated.

Molecular biology errors

From my reference file is the following entry.
Lewin, Roger.  1988.  DNA clock conflict continues.  Science, 241:1756-1759. describes article of Charles Sibley and Jon Ahlquist using DNA hybridization criticized by Vincent Sarich and others – wrong side (Sarich) seemed to win charging selection of data but Sarich Tmode used by him is selection of a worse sort. 

Sibley's work was a study of bird relationships.  He had eliminated some data that were obviously contaminated as he knew by his experience with the technique and had properly noted in his work.  His approach seems to have been abandoned, unfortunately since it avoids data selection flaws found in much recent work.

This blog's post of 5/31/2013 entitled Science screw-up No. 1 describes a major episode still not resolved resulting in an invalid interpretation of animal phyla relationships.

Missing data

Finding data that we did not know was missing is an unforeseeable event that, when found, enabled me to see some important aspects of origin of animal groups.  Many posts starting in late June 2013 related to annelid theory of chordate origin and the pogonophorans may help clarify the significance of Webb's publications about the finding of the formerly unknown segmented posterior extremity of pogonophorans.

Estimating the time of glacial retreat in Michigan based on strata of bog vegetation carbon-dated ages has developed with a possible error.  Fossil carbon of low activity was probably incorporated in bog vegetation from carbon derived from ancient carbonate deposits dissolved in water entering lakes where the plants grew.  This missing aspect of the data would give an older age to the age estimated proportional to the percentage incorporated.

The errors and other criticized findings you may find in my blog may be indicative of the value of an old saying -  that we can or should learn from our mistakes; also that if you are afraid to make a mistake you are not likely to find anything.  I thank them all, if they hadn't tried, I wouldn't have much to say.


Joseph G. Engemann   September 17, 2014

EVOLUTION

The Error of Irreducible Complexity

FALSE SCIENTIFIC CREATIONISM ARGUMENTS

Irreducible complexity is probably the most believable of the error filled arguments of "scientific creationists."  Their attempts to credit the stories of creation found in the Bible with factual scientific truth impede others from seeing the grandeur of creation with one single creative burst giving rise to the universe and ultimately the process of evolution by which life came to exist.

Darwin's Black Box, a 1996 book by Michael Behe defines "irreducibly complex" as "a single system composed of several well-matched, interacting parts that contribute to the basic function,wherein the removal of any one of the parts causes the system to effectively cease functioning."

Darwin himself provided the argument in Chapter Six of his The Origin of Species entitled "Difficulties of the Theory".  Darwin's first sentence of a sub-section "Organs of extreme perfection and Complication" reads as follows.

"To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree."

Why the seeming absurdity may not be absurd is discussed for three pages before the sub-section concludes with the following sentence.

"Let this process go on for millions of years, and during each year on millions of individuals of many kinds; and may we not believe that a living optical instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?"

In the century and a half since Darwin presented that view, morphological and molecular evidence has accumulated that make it easier for informed biologists to understand major steps of the process.  The basic ultrastructure of the eye's retina associated with derivatives of cilia probably began with light sensitive spots on roots of cilia or flagella enabling photosynthetic flagellates to give a directional response to light when shaded by an associated pigment granule.

Most of the above is found in chapter two of my 2010 Evolution Insights manuscript which includes the following statement.

"The fact that an eye cannot function well with an essential part removed does not mean that it could not evolve gradually from one that did not have that part.  Because God did create it, either by the evolutionary process or by some more recent creative event should be answered by the facts if such exist.  Those believing in God as their creator should stop to think that God is the creator of all things either directly or by the natural processes of the one created world.  The consequence of that, a world behaving according to God's laws, is that there is truth in the correct interpretation of the evidence the world presents."

Joseph G. Engemann     September 15, 2014

CREATIVITY: Last First

The Two Way Street

Was the name of my 1974 manuscript on creativity which was never published.  Since it dealt with creativity and the value of reverse viewing, I am starting at the end with a series of cartoons it contained.

The caption "Don't say anything, he thinks he's creative." was a jab at myself.  Perhaps it was a reminder to not take myself or my ideas too seriously.  The cartoon followed the final chapter, number 13, which did not particularly talk about how to be creative, but reviewed some ideas I had entertained that did not appear in earlier chapters.

An idea for improving certification processes for teachers and my realization that administrators can be an effective source for good preceded ideas I thought important to work for as a congressman.  I did not run for congress in 1969 after thinking about it and discarding the idea.  An example of one idea entertained was the following in a section on "Social Needs."

"There were programs I was interested in pushing that were dubious campaign issues because of complexity or the potential for misunderstanding or arousing effective opposition.  As a university teacher I enjoyed a retirement program (TIAA-CREF) where my rights were immediately vested and could be taken from job to job.  Why should not all workers have that advantage?  It is especially irritating to see corporations rob older workers of their pensions by either mismanagement or corporate restructuring.  So a federally licensed pension system similar to TIAA-CREF should be a right of all."

Permission to use the above cartoon in non-profit publication or personal use is granted with the hope you will credit evolutioninsights.blogspot.com

Joseph G. Engemann    August 18, 2014

EVOLUTION: CIRCULATION

THE CIRCULATORY SYSTEM

Circulatory systems have evolved and transport things throughout the body.  So transportation is the primary function, but the things transported can be oxygen, nutrients, waste products, and molecules serving a variety of functions.  The transport of many of the substances could be accomplished by a fluid filled body cavity, or just cell to cell in very small organisms.

The need for oxygen in active large animals is greater than can be transported by oxygen dissolved in body fluid of large animals.  So respiratory pigments such a hemoglobin allow a much greater supply of oxygen to be transported rapidly. When oxygen is abundant in the just inhaled air in the lungs it will combine with hemoglobin, but when it reaches tissues where it is depleted it is released.   Typically, the depletion is due to metabolism resulting in production of carbon dioxide which is then carried on the return trip to the lungs for release and elimination with exhaled air.

Circulation of blood in animals with heart, arteries, capillaries, and veins is like a bus route.  Some things go round and round on the route.  Others, such a hormones may go round and round until they are bound up by the target organ.  Those control substances included things that stimulated or inhibited processes in the target organs.  Over time delivery of control substances for specific targets selected processes that became the nervous system enabling precision in control.  But longer acting processes where instantaneous response is not important are adequately served by the circulatory systems of organisms.

EVOLUTION OF THE CIRCULATORY SYSTEM

No circulatory system
Many students have had the opportunity to see circulation within cells while observing Amoeba, Paramecium, or plants such as Elodea with  microscopes.  Similar cytoplasmic movement can occur in animals with circulatory systems.  Movement of the organism can provide some functions of a circulatory system by leaving waste behind as areas with more oxygen and food are reached.

Gastrovascular type circulatory function
Animals in the phylum Cnidaria (jellyfish, corals, and related forms) and Platyhelminthes (flatworms) are the major groups with gastrovascular type systems.  The name comes from it being the central digestive cavity which may be branched reaching all the parts of the body and having the capacity to carry on digestion as well as circulation enhanced by body movements and sometimes cilia.

Body cavities as circulatory systems
In the previous types the space between the epidermis covering the body and the organs such as gonads and guts are filled with either mesoglea (jellylike material and few cells) or parenchyma (large water-laden cells) through which materials can diffuse, but where little metabolic work is done.  The simplest body cavity to contain organs is called a pseudocoel because it lacks a lining of epithelial cells as in those with a coelom (as found in all eucoelomate higher phyla).

The importance of the coelom for provision of circulatory function is indicated by small organisms such as the bryozoans.  In the photo below of several polyps (or zooids) of a colonial species, Pectinatella magnifica, the particles in the space between gut and body wall are circulated with the body fluid propelled by patches of ciliated cells on the lining.

Body fluids of many organisms such as the above also serve a skeletal function of support for the body when fluid is confined within the body and compressed to keep the organism inflated.  The exact evolutionary relationship of the bryozoans is not certain.  They are a very old group that may have no close ancestry to advanced phyla, or they may be derived from more advanced forms due to reduction much as occurred in the pogonophorans.

Blood vascular systems as circulatory systems
The origin of the blood vascular system is speculative.  It seems consistent with the gradation seen in animal complexity that the lateral branches (or a dorsal branch) of the digestive system seen in flatworms took on another function as the animals grew longer and developed an anal opening for the central branch.  Over time
muscles providing peristaltic movement of contents were gradually converted into hearts as needed.  The annelid worms and the fishes provide examples of some of the steps along the way to the system seen in mammals.

Blood of vertebrates
Blood cells of vertebrates are often categorized as white blood cells and red blood cells.  Most vertebrates, including fish, amphibians, reptiles, and birds, have large, nucleated, football-shaped red blood cells. Mammals have small red blood cells that are flattened disks (usually characterized as biconcave disks) that lack a nucleus when mature.  Vertebrates have hemoglobin in their red blood cells and thus help keep the viscosity of the blood lower.  The cells, in addition to lowering blood viscosity, may help improve the transfer of materials in the capillaries of organs by making the whole fluid column in the capillary move at the same speed.  The wiping action, in effect, reduces the diffusion distance for materials being exchanged.

[Note  added June 3, 2015: An important part of circulation in vertebrates is thought to be escape of water and smaller solutes, including oxygen, from the arterial end of the capillaries into the interstitial fluid; uptake at the venous end of the capillaries returns much of the fluid, and carbon dioxide; and solutes and fluid that cannot be taken back by the venous end may return to the circulatory system via the lymphatic vessels.  This circulation pattern is driven by higher hydrostatic pressure in the arterial end versus lower pressure in the venous end as well as the higher remaining concentration of larger solute molecules in the venous end.]

Blood particles, called platelets, are important in clot formation that seals off breaks in the blood vessel walls.  White blood cells are of several types important in function of the immune system.  These constituents of blood are formed in marrow found inside bones of the body.

Joseph G. Engemann         August 6, 2014

EVOLUTION: SPATIAL DIMENSIONS AND NATURAL SELECTION

NATURAL SELECTION

Survival is affected by many different things.  This post will discuss the impact of length, surface, and volume on natural selection.  Such simple physical components of an organism can have great affect on the organisms relationship to its environment as well as to physiological and mechanical functions.  The fourth dimension, time, is certainly an important component of natural selection but it is not discussed in this post.

THE LINEAR DIMENSION AND SURFACES

If an animal only grows in one dimension, length, its mass is directly proportional to its length.  Some subterranean animals find this a way to get bigger without required larger dimensions of tunnels they occupy.  For attached, or sessile, animals increased length gives them access to food items farther away from an area proportional to the square of the distance.  Surface area of the organism, ignoring the factor of tapering ends usually involved, increases in proportion to the product of length and width or circumference.  For a flat, encrusting type organism, that doubles in length and width of surface dimensions, the larger form has four times the surface area.

VOLUME OR MASS

Of course, organisms all have a third dimension, depth or the dimension at right angles to both length and width.  The product of length, width, and depth gives the volume or mass of the organism.  Organisms with complex shapes can have their volume calculated from the sum of volumes of all their parts.  A simpler measure can be equivalent to the volume of water displaced when it is immersed; its weight is also a good approximation, if it lacks mineralized parts each gram equals approximately one cubic centimeter.  The animal that doubles each dimension has volume or mass increased from one unit volume to eight units of volume as illustrated below.

THE PRACTICAL CONSEQUENCES OF INCREASED SIZE

The inequality of the ratio of linear, surface, and volume measures has great impact on design of animal bodies produced by natural selection of genetic variations.  If shapes are identical, linear measures are directly proportional to length, surface areas are proportional to the square of the linear dimension, and volume or mass is proportional to the cube of the linear dimension.

Rates of delivery of materials to and within organisms varies greatly due to variations in permeability of membranes, circulation of protoplasm within cells, binding with other molecules, circulatory systems, surface area modifications, and additional chemical and physical factors.

Mass or weight

Dinosaurs were thought to be near the maximum size for a terrestrial organism because the mass increased with the cube of the linear dimensional increase whereas the strength of the skeletal support in leg bones only increased with the square of the diameters of the bone.  If they grew bigger they would need bones too big to be contained within the organism.  Likewise muscles to move the mass increased in strength proportional to their cross-sectional area and reached the limit of practical size; muscle and bone would be unable to keep up in needed strength for greater size.

Birds, and presumably some dinosaurs, have hollow leg bones that have greater strength with less increase in weight.

The increased size of most advanced animals made the ratio of length to surface area of organs exchanging nutrients, oxygen/carbon-dioxide, and heat from body surfaces, lungs, and gut have survival improved when gills, pouches, folds, and other mechanisms increased the surface without increasing overall size.  An example is the longitudinal fold called the typhlosole in the gut of the earth worm.  The Tasmanian isopod also had a typhlosole.  However, the worm has it in a dorsal position and it has more internal structure.  The isopod has it in ventral position and it is simple in structure.  In the first picture below, the typhlosole is projects up from the bottom of the tubular gut- which has some food included.

Such modifications enabled animals descending from flatworms achieve thickness and complexity.  Flatworms are limited in thickness in part by the inability of sufficient oxygen to diffuse to active tissue more than a few cells away from the surface.

To enable many of the advances to take place, a circulatory system was necessary to effectively take out most of the need for diffusion over the distance from surface of uptake to surface of release of transported nutrients, wastes, and oxygen.  Hemoglobin and other respiratory pigments enabled greater quantities of oxygen to be transported because the combined form of oxyhemoglobin did not contribute to oxygen saturation of blood fluid.

The dorsal blood vessel and heart are shown above the gut in the two pictures below.  In the first picture arteries, labeled A are going off to each side; in the second picture the heart shows an ostium (O), the valve through which blood enters the heart from the hemocoel (the blood filled body cavity that serves the role of capillaries and veins in arthropods).

The arteries carry blood to the thin-walled pleopods, abdominal leaf-like appendages with thin walls where oxygen and carbon dioxide are exchanged with the surrounding water.  The blood then carries oxygen to the various tissues of the body on the way back to the heart.  Along the way it picks up nutrients absorbed by the gut, eventually entering the heart through the ostium.  The blood bathing the internal spaces does the job of capillary networks in higher organisms.

The gut of the Tasmanian isopod has very large cells lining it.  The photo below is an enlargement of the gut or intestinal lining (I) where it meets the rectum (R) lined with small cells.

Larger organism have greater complexity and require proportionally larger muscles and capillary networks as a result to insure adequate circulation.  Such things allow them to overcome the decreasing rate of provision of needed substances and removal of wastes found with diffusion based circulation that is adequate for microorganisms. 

[Photos are from Engemann, J. G.  1963.  A Comparison of the Anatomy and Natural History of Colubotelson thomsoni Nicholls, a South Temperate, Fresh-Water Isopod and Asellus communis Say, a North Temperate, Fresh-Water Isopod.  Ph.D. thesis, Michigan State Univ., East Lansing.  146 pp.]

Joseph G. Engemann           August 4, 2014