18. Speciation: The division of a population into separate, distinct, and re productively isolated groupings involves significant alterations in genes, although the amino acid changes may be quite small. The two methods by which speciation occurs are:

1) Allopatric speciation [two populations are geographically isolated and over time evolve into different species].

2) Sympatic speciation [one species splits in two when a small proportion of individuals within a population reproduce exclusively with each other]. Sympatic speciation–more common in plants than animals–is rarer than allopathic speciation and may be the result of non-random mating or a mutation that leads to reproductive isolation. Geographic isolation is not necessary for this division within a population. Both may demonstrate either or both postzygotic hybrid sterility or inviability (mules are the sterile offspring of horses and donkeys). There are also prezygotic isolating mechanisms: habitat isolation, temporal isolation–organisms breed at different times–behavioral isolation–incompatible courtship rituals and other mating cues, mechanical isolation–incompatible genitalia–gametic isolation–gametes cannot fuse at the time of fertilization.

There are two forms of sympatic speciation that are worthy of mention, but will not be described in depth. They are allopolyploid speciation and autopolyploidy. Allopolyploidy does not begin with physical separation of populations, but rather it starts with hybridization of two different species which occupy the same territory. The process requires that each species’ chromosome types and/or numbers differ from the other species. Proper pairing cannot occur and any offspring will be sterile. However, if both species’ chromosomes double–which, strangely enough, is not rare–they then have pairable chromosomes and can produce new, viable, and fertile offspring which is by all definitions a new species, one that is incapable of successful breeding with either of the parental species. Autopolyploidy occurs when a single species doubles its chromosomes, again not a rare phenomenon, in fact a common one. When such an organism pairs with another organism from the same species which has doubled its chromosomes, viable offspring result. However, neither the organism with the doubled chromosomes nor the offspring of such a mating will survive and be fertile. For either type of event to occur a rare event has to occur in two generations. The remarkable thing is that such events are not rare in organisms that have a rapid generational turnover in a large population. Single plants produce millions of eggs and pollen grains making such an improbable event become probable. Autopolyploidy is so common, in fact, that it is estimated that 70% of all extant plants had a polyploidy event occur sometime/somewhere in their ancestry and is a common way that plants speciate (except for trees). Polyploidy is much rarer in animals, but does occur occasionally in fish, insects, worms, and reptiles. The red viscacha rat of Argentina has 112 chromosomes.

Large chromosomal rearrangements such as the fusion of two chromosomes in the chimpanzee/human ancestor that produced the human chromosome 2 do not necessarily change gene function, but do generally result in reproductive isolation. In a study of the lungless salamander, Ensatina eschscholtzi, the classical Darwinian process of natural selection leading to evolution and finally to speciation that is even currently in progress is clearly elucidated. The study, Patterns and Processes of Species Formation in Salamanders, by David B. Wake, published in the Ann. Missouri, Bot. Gard. 93:8-23, 2006 revealed that the deciding factor in that animal group was geographic isolation. If individuals become geographically isolated from members of their populations, any mutations occurring in these isolated individuals will further remove them genetically from the original population. With sufficient divergent evolution, the groups, if brought into physical contact, may not be able to produce offspring; and if they are able reproduce, the offspring may be sterile. Some other changes that might accomplish this are:

1. ~seasonal incompatibility (different breeding seasons preclude cross-copulation).
2. ~Environmental isolation, e.g. pollination by bees versus hummingbirds due to flowers living in different areas with attendant evolutionary changes to accommodate the different selection pressures plus mutations.
3. ~behavioral incompatibility (nonmeshing courtship rituals).
4. ~gamete incompatibility (sperm and eggs from different groups cannot form a zygote).and embryo mortality (the zygote cannot develop past a premature state).

Dr. Wake’s research involved studies of the salamanders’ enzymes, and nuclear and mitochondrial DNA which demonstrated the underlying genomic evidence of a species complex breaking up—evolutionary development. continued…

Classical science is based on the belief that there exists a real external world whose properties are definite and independent of the observer who perceives them. According to classical science, certain objects exist and have physical properties–such as speed and mass–that have well-defined values. In this view, theories are attempts to describe those objects and their properties, and our measurements and perceptions correspond to them both. All other observers who look will measure the same properties, and the object will have the same properties whether anyone observes them or not. In philosophy, that belief is called realism.

An example of the scientific method offers a refutation of the irreducible complexity argument from creationism. That argument holds that a hormone and its receptor cannot have come about through evolution. Joseph Thorton, et. al, working at theUniversityofOregon, reconstructed an ancestral receptor and using the process of gene resurrection, worked backwards to infer what the gene was for in the ancestral receptor, a molecule that existed 450 million years ago. They found aldosterone and another hormone that both fit the ancestral receptor which was fully functionally employable as the “keyhole” for the second hormone. Aldosterone appeared by random mutation and co-opted the existing receptor. Scientists argue that bacterial flagellae and the lens of the eye could also have evolved by the same process of co-opting the pre-existing structure.

17. Sexual Selection and Evolution: Sexual selection theory, as part of evolution, allows for testable predictions. With the rarest of exceptions, if a species shows sexual dimorphism in which only one gender (almost always the male) shows brilliant plumage, dramatic antlers, imposing size, performs impressive mating rituals, makes more dramatic calls, or builds elaborate structures to lure the opposite sex (almost always the female) into acceptance of sexual advances, the more elaborate or ingenious sex will be in active competition with other members of the same sex. Species showing less sexual dimorphism, such as penguins and geese, show less such behavior and are more likely to be monogamous and to exhibit sexual fidelity.

There are exceptions to the finding that it is the male that is the most beautiful and alluring, and these exceptions further make the point indicated above. In sea horses, for example, it is the male that fertilizes and carries the brood of eggs in a specialized pouch—becomes pregnant—and has a longer gestation period than it takes the female to produce a new batch of eggs. Males, therefore, invest more in child bearing than females among sea horses. As would be predicted by evolutionary theory, the female is the more highly decorated with brighter colors and more ornamentation and competes for the favors of males. Phalaropes, shore birds that breed in North America and Europe, have a polyandrous mating system (one female and many males). Males are responsible for nest building, child care, and feeding of the young while the female moves around mating with other males. Again, the male’s investment in offspring far exceeds that of the female, and she must compete for the favors of other males. As predicted, in phalaropes, the females are by far the most brilliantly and beautifully colored.

This correlation of sexual dimorphism and competition is predictable and explainable only by the principles of evolution. Creationist explanations offer no rational alternative theory. The fundamental question is: why should there be a correlation between sexual dimorphism, with all its elaborate displays and ostentation, except to further the process of evolution by the enhancement of sexual reproduction of the fittest individuals and the strengthening of the species? The well-tested answer from evolution is that the less ornamental sex–usually the female–gains in two ways from having the privilege of choice. First, directly, the female gets to choose a fitter male to produce more and healthier offspring in a safer and more propitious environment guarded by the male during the period of child care. Second, indirectly, the female secures better genes for her offspring and therefore an advantage in the next generation.

Evolution Blogspot 6. Expanded Definitions, Part V

And both that

morning equally lay

In leaves no step

had trodden

black,

Oh, I kept the

First for another

day!

Yet knowing how

way leads to way,

I doubted if I

should ever come back.

–The Road Less Travel By–

-Robert Frost

            The culmination of the many factors that result in evolution and the production of the great plentitude of species on Earth is the division of the descendants of a common ancestor into distinct and separate species. In the course of life of plants and animals there have been millions of different species that have evolved, and more than 90% of them have become extinct. Considering all domains of life, it is estimated that there are about 8.7 million species globally, of which about 2.2 million are marine creatures. Despite 250 years of taxonomic classification and over 1.2 million species already catalogued in a central database, evolutionary scholars suggest that some 86% of existing species on Earth and 91% of species in the ocean still await description. These same experts calculate that between 0.01 and 0.1% of all species will become extinct each year. continued…

   To understand evolution, one must realize that evolution is almost never about an individual; and it is almost never abrupt—occurring in one generation. That implies that one must understand what happens to whole populations—to see the forest, and not just the individual pine trees.

14. Population Genetics: The Hardy-Weinberg Theorem states that the genotype and allele frequencies of a population will remain constant from one generation to the next if the population has the following characteristics: large size, no gene flow into or out of the population, no mutations, random mating, and no natural selection. A population that meets all of those requirements is described as being in Hardy-Weinberg equilibrium and is not evolving. Of course very few populations are ever in such strict equilibrium. Population geneticists construct a theoretical H-W equilibrium and compare it to the real state in nature. A deviation from the state of equilibrium is evidence that the population is adapting and that the process of microevolution is taking place. Molecular biologists–evo-devo scientists–can look into the genome of the members of the population to determine what alterations have occurred that are establishing that change.

 The two allele Hardy-Weinberg equation is p2+2pq+q2=q2+1, where p equals the frequency of allele A; q equals the frequency of allele B; p2 equals the frequency of genotype AA; 2pq equals the frequency of the prototype AB; and q2 equals the frequency of the prototype BB. Each organism contains two alleles, either a homogenous pair (for example, AA or BB), or a heterogeneous pair (for example AB). Geneticists can determine the frequency of one allele given the frequency of the other. According to the Hardy-Weinberg equation, the combined frequencies of the two alleles—the frequency of allele A (p) plus the frequency of allele B (q)—must equal 1. Because p+q=1, if the value of p is known, the value of q is found using the equation q=1-p.

                The processes involved in developing, maintaining, or changing populations and eventually resulting in speciation and evolution are:

• Gene amplification: an increase in the frequency of replication of a DNA segment, which may be induced by a polymerase chain reaction.
• Gene drift: unpredictable, chance changes in allele frequencies that cause one allele to become more common in a population than another allele. Drift may occur slowly over time or may come about due to a sudden decrease in population size.
• Gene flow: the alteration of the frequencies of alleles of particular genes in a population, resulting from the interbreeding with organisms from another population having different frequencies.
• Gene frequency: the frequency of occurrence or proportions of different alleles of a particular gene in a given population.
• Gene pool: the total genetic information in the gametes of all the individuals in a population.
• Gene transcription: the genetic information in DNA is transcribed or rewritten onto a strand of messenger RNA (mRNA). Transcription occurs when DNA is unwound, and one strand serves as the template of mRNA.
• Gene translation: during translation, the information on the mRNA is used to assemble a new protein. During translation, the three base sequences on the mRNA called codones specify the sequence of amino acids to be assembled in the creation of a specific protein. Ribosomes assist in protein synthesis by serving as docking points for tRNAs–amino acid-carrying molecules that bond to the mRNA condone.
• Gene expression: the synthesis of proteins according to information encoded in DNA. The timing and frequency of gene expression is controlled by many factors in the cell.
• Gene regulation: In prokaryotes, the regulation occurs via activators and repressors that promote or reduce transcription. In eukaryotes, regulation occurs via both transcriptional and posttranscriptional control. Proteins called transcription factors are required for transcription to begin, and proteins called enhancers activate transcription. The mRNA is processed after transcription. Introns are spliced and a cap and tail are added to the mRNA.  Posttranscriptional controls in eukaryotes include RNA splicing, transporting the mRNA out of the nucleus, selective destruction of mtRNA, selective destruction of proteins, and selective translation of mRN.

16. Science: Science is an active discipline wherein working hypotheses are put forward and facts are accumulated to develop a concept and finally are sufficient to support or refute a theory over time until the theory achieves a level of validity to be considered a fact or a law of nature. For example, the physical theory or law of gravity related to the attraction of two objects proportional to their mass—the first force to be described in mathematical terms–or the chemical theory or law defining water as a combination of two parts hydrogen united with one part oxygen on a molecular level are firmly established and considered to be irrefutable. In science–as opposed to religion or science fiction–experiments must by performed, and the methodology of those experiments must allow for disapproval and negation of the hypothesis as well as providing positive proof of the correctness of the hypothesis. Knowledge from experimentation may lead to new ideas and explanations that reveal the incompleteness or deficiencies of previous explanations. Doubt in science is considered crucial to finding the truth; whereas, in religion, doubt is usually considered to be inappropriate or outright anathema. continued…

The next crucial component of Darwin’s theory–and one that will be discussed even more fully in the blogspot about human evolution—is the concept of the common ancestor:

5. This is the fourth basic tenet of Darwin’s Theory. Scientists study common ancestry by tracing fossils, phenotypy (morphology), and genetic profiles backwards. The most obvious observation is to establish nested hierarchies, e.g., fish, amphibians, reptiles, and mammals all have a back bone, i.e., they can be naturally classed as vertebrates. Classes such as vertebrates can be broken down into further nested hierarchies—mammals into whales and primates, primates into monkeys and apes, apes into chimpanzees and humans, etc. Even without introducing the refinements of DNA, evolution is apparent in these nested hierarchies. By comparing the DNA sequences in the chromosomes of two later species, biologists can determine the genetic changes that have occurred since the known organism that served as the common ancestor. The more similar the DNA sequences, the closer in time are the newer species and the common ancestor. By that deductive reasoning, humans are closer to chimpanzees, or rather to a common ancestor of both species, than we are to baboons, monkeys, or fish, etc. Based on DNA evidence, the common ancestor of humans and chimpanzees lived in Africa about 6-7 million years ago (MYA).

            Unlike the creationist concept where organisms are generated as a finished whole and all at once, the common ancestry concept, a testable theory, demonstrates change over time starting with an organism that changed—evolved—and only partially resembled the organism as it appears today. For example, noting that birds and reptiles share certain important physical characteristics and significant similarities in DNA sequencing, it is reasonable to predict that a common ancestor existed that had evidence of characteristics of both. That is a fact—fossils that correspond to a given and predicted period of time have been found that are unmistakably ancestors of both classes of organisms.

6. Conservation of Genes and Proteins: It is an integral part of the parsimony and frugality of the evolutionary process and hinges, to the point of being a law, that mutations that produce changes that enhance survival of the species persist, and those that do not enhance survival die off and do not become part of the heritable gene pool. By finding conserved genes, it is possible to infer with considerable accuracy, a linkage to a common ancestor, e.g. from invertebrates to vertebrates.

            In fact, the rule of conservative changes states that only those changes can be tolerated that essentially change nothing. This rule applies to any set of interacting elements where changes in any one component will alter all of the interactions in which this component is involved, and adversely affect the function of the entire set. Biological organisms all undergo a developmental process that leads from the embryological zygote to the adult reproductive stage. The rule of conservative changes implies that any mutational change is first and foremost screened for its compatibility with every step in the developmental program. This is because the only absolute requirement is that the entire program remain functional and retain its coherence.

7. Convergent evolution is an independent evolutionary development of traits. Although reptiles developed flight 75 million years before birds, the components of evolution involved were much the same. However, insects developed wings much later than birds and along an entirely separate genetic/evolutionary track—and example of convergent evolution.

8. Deoxyribnucleic or Deoxynucleic Acid (DNA): Containing, as it does, the three dimensional double helix blueprint for all heritable information, DNA serves as an archival medium for genetic information both ancient–including genes that are over a billion years old and unchanged–and more recent ones, with the ongoing record of mutations. DNA’s properties are the basic ingredients of cumulative selection and directional change in populations over time. Much of DNA, however, is nonfunctional, even fossil, in that it contains changes that were of neutral survival value and changes that were once important, but have since been replaced by more adaptive gene mutations. DNA that is crucial is preserved with remarkable felicity over time; and genes and proteins with less exacting requirements undergo mutations, but persist in somewhat degraded forms. For example, fibrinopeptides are proteins produced during the clotting of blood. They are among the most rapidly evolving of all molecules because they are ignored in the process of natural selection since their function can occur with a rather wide range of amino acid configurations.

            The fossil or non-functional components of the DNA pool are re-arranged and even scattered about in the organism through time, but they remain present and can be re-activated to form the useful functions required by a newly arisen adaptive requirement; such is the frugality of the processes of DNA function and of the resultant evolution; proteins and genes are used, reused, and used for different, sometimes radically different, functions.

            DNA replication is the process by which the two strands of DNA are separated, each strand serving as the template for the formation of a new strand. There are three types of DNA: Chromosomal or nuclear, Y Chromosome, and Mitochondrial or cytoplasmic.

i. Chromosomal or nuclear DNA has the blueprint data for most body structure and is inherited half from each parent. This type of DNA also contains considerable non-functional material, but even this “fossil” DNA is passed on and may undergo mutation.

ii. Y Chromosome DNA lies on the chromosome and determines male sex. It can be used to study evolution in males only, but is fairly difficult to study in the laboratory.

iii. Mitochondrial DNA (mtDNA) is found in cells outside the nucleus. It is inherited through females only. Owing to its cellular location, it is comparatively easy to extract, isolate, and study.

9. Gene: Genes are chemically–not electrically–encoded in digital-like fashion in strictly maintained orders and sequences on different lengths of nucleotides and serve different functions. The encoding process is ROM (Read-Only Memory); that is, the process is capable of being read millions of times, but it can only be written to once. The unique information encoded in each gene corresponds to the synthesis of RNA and thence to the manufacture of proteins, made up of amino acids linked together in long chains. There is a direct correspondence between the sequence of bases in DNA and the sequence of amino acids in proteins. The mammalian and human genomes contain about 25,000 genes. Despite the myriad of functions throughout the living world brought about by these genes, the genetic code for proteins is only a twenty word vocabulary. The sequence of amino acids in each protein determines their function—e.g. carry oxygen, form muscles, break down glucose, form electrical synapses, etc. Inheritance is not by the biblical mixing or blending of “blood”, but by the transmission of the information that is particular and in discrete particles. Humans are females or males, not a gradated blend of both–an hermaphrodite. The same is true for every particle (gene) we inherit. There is a shuffling and re-shuffling down the generations, but the genes remain separate and distinct as they are parceled out from a male and a female to their offspring with some of the genes going into the new zygote from each contributor.

10. Homology: A homologous trait is a unique historical change in the developmental program of an evolving lineage. Homologues may be different appearing and functioning structures in a wide variety of animals but are the same structure modified from the same genes in different ways in the different species. (See conservation).

          Limbs, wings, gills, and antennae are serial homologues that arose as a repeated series which became differentiated from simple repetitive ancient limbs through genetic mutations and handed down to offspring in the different species, e.g. the five fingered arm plan seen as Tiktaalik’s altered fins, in bat wings, and in the dexterous human hand. Human teeth include a variety of different kinds of teeth reflective of our retention of the original genes and of the evolution of our complex and successful form. It is striking to discover that many of the genes critical for early brain development are homologous between insects and vertebrates. Indeed, the invertebrate and vertebrate genes are sometimes functionally interchangeable.

It is important to note that developmental, structural, positional, compositional, and functional features of phenotypes as well as genomic features are all useful in proposing hypotheses of phenotypes. Only features that can be traced to a common ancestor in an explicitly phylogenetic context are regarded as homologues. Congruence in the phylogenetic distribution of numerous character states is regarded to be the ultimate evidence for homology.

11. Hox Gene: Very similar Hox genes are found in a myriad of different animals producing related but very different outcomes in the derivation of form. There is a large compendium of evidence attesting to the presence of Hox genes in ancient ancestral creatures that are preserved and still function in modern animals confirming the subtlety and nuanced incremental nature of changes produced by mutations acting with frugality on an ancient framework with fundamental DNA based structures.

There is a very vigorous protective function in the DNA transmission process. Let one example suffice: Cows and peas–indeed, most of the earth’s flora and fauna–have a nearly identical gene, histone H4. Its DNA text is 306 characters long in both cows and peas, and the nucleotides and their order differ by only two characters between them. Evolutionary Developmental studies involving correlation with fossils indicates that the last common ancestor of peas and cows lived between 1,000 and 2,000 million years ago, an unfathomably long time. After that time, each of the two branching lineages from that ancient ancestor preserved 305 of the 306 original characters. The preservation was a dynamic activity because with every new generation, DNA had to replicate the characters with exactitude—over an estimated 20 billion replications. The replication-reservation process is all the more remarkable because during that 1.5 billion years or so and 20 billion replications, the organisms were all subjected to the pressures of natural selection and mutations.

The reason for such faithful and prolonged preservation of the exact genetic information of histone H4 gene is that it is crucial to the structural engineering of chromosomes. About 5,000 DNA characters degenerate every day in every human cell and are immediately replaced by repair mechanisms so efficient and exacting that the lifetimes of DNA messages are measured in millions to hundreds of millions of years—a range of 10,000 to trillions of lifetimes. Even without the processes of natural selection in force, DNA replicates so accurately that it takes five million replication generations to miscopy even one percent of the characters. Thus, Hox genes have survived over thousands of millennia in a host of different organisms.

12. Hypothesis: A not fully proved or even adequately studied assertion which occupies a position of scientific acceptance well below the status of a theory. An example of an hypothesis–more accurately, hypotheses–related to The Theory of Evolution by Natural Selection relates to how self-replicating–i.e. living–organisms could form and begin to evolve. Recreating conditions that led to the earliest such organisms is extremely difficult because much remains unknown about the chemical and physical characteristics of early earth. Researchers have proposed many concepts—hypotheses about how life began—but none of these hypotheses has yet achieved consensus, much less the production of life in a laboratory. It is now hypothesized that for life to begin, three conditions had to exist: First, groups of molecules that could reproduce themselves had to come together. Second, copies of these molecular assemblages had to exhibit variation so that some were better able to take advantage of resources and withstand challenges in the environment. Third, the variations had to be heritable, so that some variants would increase in number under favorable environmental conditions.

            The most promising work on hypotheses related to the inception of life is coming from the study of ribonucleic acid (RNA). RNA is related to DNA and similarly consists of nucleotide subunits in chains. The molecule serves a number of cellular functions, including providing a template for the synthesis of proteins and catalyzing certain biochemical processes. Viral processes involve RNA and act in a simple way to function within cells, usually in a destructive manner. The viral functions are dependent on the cell, and hypotheses are under development to experiment about the possibility of a link to early life processes that may have become independent.

            An example of such work is that of the German group headed by Manfred Eigen and is described by Richard Dawkins in his book, The Blind Watchmaker, page 133. The scientific paper is, Eigen, M., et. al., The Origin of Genetic Information, Scientific American, 244 (4): 88-118, 1981. It was known beforehand that a test tube containing RNA, the chemical building blocks of RNA, and the enzyme, replicase would produce replicating RNA, a combination which occurs in viral cells living in bacterial cells and in the cells of other organisms. Eigen and colleagues performed an experiment in which they placed replicase and the chemical building blocks together in the test tube but left out the RNA. A large RNA molecule evolved spontaneously in the test tube, and the same molecule replicated itself—re-evolved—multiple times in subsequent independent experiments. The remarkable thing about this experiment is that a large self-replicating molecule was produced even though the statistical probability of producing such a molecule more than once by chance was very highly improbable. Crude evolution is seen in the test tubes when mutations occasionally occur in the automatically produced RNA which is capable of making better RNA copies, and still better future ones by powerful processes of cumulative selection.

            The flaw in the study is that the very particular environment of the experiment was created in a test tube under carefully controlled temperature and with ready-made replicase without any real knowledge of precise conditions in the dim past of the earth, whether such conditions as were found in the test tube were ever in existence, or whether replicase has ever come about spontaneously, and if so, how could it have come into contact with the exact components in the correct proportions to produce RNA building blocks. This and similar work is suggestive, but the evidence is inadequate to afford such limited findings the enhanced status of being a theory. It is important to bear in mind that the requirements for a concept to be labeled a theory of science are very stringent.

13. Mutation: There are a wide variety of physical changes in genes that constitute mutations:

i. Point mutations in which one base is substituted for another,

ii. Regional chromosomal mutations in which a whole region may be deleted, moved or duplicated; and amplification of duplicated regions in which the mutated regions may grow into a long, multiply repeated set of identical protein sequences by unequal exchange between homologous chromosomes,

iii. and a number of other gene alterations including inversions, translocations, transpositions, and inversions with movement to another chromosomal location. Such modifications can alter the regulatory connections in the genomic system.

            Most mutations are neutral and do not change function or heredity; or they are negative, leading to death or functional failure and are lost to heredity. Only a very few mutations enhance adaptability and go on to improve a population’s survivability over time.   Mutation rates vary significantly and depend to some degree on environmental stresses such as exposure to mutagens like x-rays, toxic chemicals, cosmic rays, radioactivity, and even other genes known as mutator genes. Different genes have different susceptibility to and likelihood of mutation. For instance, the rate at which mutation causes Huntington’s Chorea–an invariably fatal dementing disorder characterized also by dance-like writhing movements and behavioral disturbances–is about 1 in 200,000, and the rate of mutation in the gene which causes achondroplasia–a type of dwarfism–is ten times greater.

14. Natural Selection: Environmental factors facilitate divergence from the ancestral form in species. These phylogenetic changes usually involve small incremental changes in physical form or function which can be especially dramatic when an evolutionary change enables a group of organisms to occupy a new habitat or make use of resources in a novel way, i.e. a better organism, one more efficient at self-replication; and over time, a new, more successful population dominates. Sufficient differences may lead to the development of a new species; in sexually reproducing organisms, species consist of individuals that can successfully interbreed with one another and usually not with other species, even the ancestral ones. Selection achieves and maintains complex systems poised on the boundary, or edge, between order and change and is based on a combination of chance and necessity.

            This concept was first proposed and based on science by William Charles Wells, M.D., an American born physician, in a paper written in 1813 which was published in 1818 regarding “Some observations on the Cause of the Differences in Colour and Form between the White and Negro Races of Man”. He observed that the Negro races were better suited for survival in the African sun, and that suitability was passed on by a process of natural selection. Forty years later–without knowledge of Wells’s work–Charles Darwin elucidated the formal theory that has been associated with him ever since.

From an extensive set of academic disciplines comes the established core concept of natural selection, the central idea that explains design in nature. Among those fields of endeavor are ecological genetics, human evolution, molecular evolution, phylogenetics, anthropology, paleoanthropology, genome studies, MRI scans for evaluation of changes inside brain cases, supercomputer re-creation of ancestral gaits, bioinformatics from mathematical disciplines, physics, chemistry, geology, astrophysics, paleontology, paleoclimatology, behavioral and social sciences, evolutionary biology, evolutionary developmental biology, biological anthropology, physical anthropology, computer iteration (e.g. Avida makes digital organisms at Michigan State University), population genetics, and probably some this writer has overlooked.

            The requirements of evolution by natural selection are that there be:

1. random genetic mutation (permanent transmissible changes to the DNA or RNA of a cell that inevitably occur at a certain rate in genes)
2. random gene drift (changes in allele frequency from one generation to the next due to sampling variance which leads eventually in the direction of a fixed proportion of 0% or 100%)
3. gene flow (admixture or migration which is the exchange of genetic variation between populations when geography and culture are not obstacles, rather like the process of homogenization, a process which counteracts selective adaptation), and genetic recombination (where, in the process of production of gametes
4. linked alleles on homologous chromosomes are inherited from the parents via meiotic recombination thus allowing independent assortment of alleles—mutations—to be propagated in the population until one type in a culture or population replaces another. Beneficial mutations tend to persist over generations, and harmful mutations tend to diminish thus producing an improvement in survival—in design. Some selections, such as heterozygote advantage over homozygous forms as exemplified by human sickle cell anemia, a serious blood disease found in black Africans and some white Mediterranean people and which confers strong resistance to falciparum malaria, have a mixed survival value. Evidence points to the transferal of sickle cell disease from the high malaria endemic regions of the Mediterranean down into Africa where malaria abounded.

            A particularly informative example of natural selection comes from the work of Charles Darwin himself. He set out on a five year voyage of exploration of the natural world on H.M.S. Beagle (1831-1836) whose primary mission was mapping the harbors and coastlines of South America. One the ship’s most important stops–so far as Darwin and evolution were concerned–was at the Galápagos Islands, 575 nmi west of the coast of present day continental Ecuador. There he turned his attention to finches, small seed eating birds. He discovered that the beaks of the birds were distinctly different on each of the 13 islands, and differed significantly from island to island. There were longer, shorter, harder, softer, etc. beaks but all recognizable as distinct and isolated to one island. The governor of the islands showed Darwin that the turtles on each of the 13 islands also had distinctly different shells and that it was possible to identify any turtle with its island even without knowing which island it had come from. Darwin recognized that reproductive isolation had produced distinctive differences in the animals and theorized that the environmental conditions on separate islands had caused a selection process. He later included those observations in his great treatise on evolution as the result of natural selection.

            Princeton University biologists, Drs. Peter R. and Rosemary Grant, returned to the Galápagos to study Darwin’s finches in 1973 and did research on the birds for the next 30 years, a remarkable feat of tenacity. They centered their study on Daphne Major, a bleak place characterized by sheer cliffs and no fresh water, and devoid of human interference into natural selection. The Grants documented the same 13 species of “Darwin’s Finches”. They caught and banded thousands of finches and traced their elaborate lineage, enabling them to document the changes that individual species make, primarily to their beaks, in reaction to the environment. They documented a severe and prolonged drought and found that even during the period of their study, the birds’ beaks made significant adaptations. During the drought, the birds quickly ate up all of the small soft seeds, and when those seeds were depleted, they were forced to turn to the larger, harder, and less palatable seeds. The Grants observed a profound change: the birds were larger, and their beaks had become larger, harder, thicker, and capable of consuming the large hard seeds. Later in their studies, the opposite happened. There was a period of severe and prolonged rain. This time, the small seeds predominated, and large seeds became scarce. During that period of study, the Grants observed that the beaks of their study birds had become longer and sharper, to reach the tiniest of seeds. From the beginning to the end of their study, the Grants could not predict the end result of the natural selection-evolutionary process that the birds would undergo. They studied more than 25 generations of finches—more than 19,000 individual birds–and reported one of history’s most convincing examples of evolution by natural selection which confirmed for all time the accuracy of the theory Charles Darwin proposed as he sat on the same island 142 years earlier.

The gene changes involved in the natural selection+mutation process all occur by chance. They occur by copying errors in the genetic material during cell division, by exposure to radiation, including naturally occurring cosmic radiation, and by exposure to chemicals or viruses. The process is usually a slow and relatively inefficient and wasteful one with many mutations being neutral and collecting as a steady accumulation in the species’ genome and with many adaptations going down blind and eventually fatal pathways. Gene duplications are a major source of raw material for evolving new genes in human precursors as well as other plants and animals. Chance, unpredictability, and randomness characterize the general process, and there is no element of preparing for the future needs of the species. There is no pre-defined or pre-directed goal in evolution, no pre-set linear direction (orthogenesis, a spurious teleological concept). As the environment changes, a genotype may no longer prevail and different directions occur in species.

There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one: and that whilst this planet has gone cycling according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.

                                    -Charles Darwin, The Origin of the Species

              The previous blogspot is an oversimplification of the elements of evolution. In the first place, many definitions are left out in order to keep this very complicated subject as simple as possible and yet to leave enough to convey an understanding of what evolution is and how it takes place. This blogspot selects certain of the most important concepts and amplifies them to further bring to understanding the core concepts of evolutionary processes.

1. Adaptation:It is incorrect to say that selection acts on a trait thereby leading to evolution. Selection is a passive and indifferent process with significant results, but is not a mechanism that is imposed on an organism or a species from the outside. Rather, it is a process of genes in organisms in an environment that produce better adaptations for that environment becoming more prevalent, more frequent, and resulting in better reproduction of organisms to survive in that environment. Adaptive traits—modifications–are best said to be undergoing the process. Mutations occur at random and by chance, but it is the filtering of that variation by natural selection, which is not random, that produces adaptations and imposes the order and design seen in species. Richard Dawkins described the process as “the non-random survival of random variants”. Natural selection is the cause of all adaptive evolution except for that produced by genetic drift.There are a multitude of examples that could be chosen to illustrate the process, but let three suffice:

i.            ~The Asian giant hornet–four inches long, two inches around, with a three inch wing span, armed with huge clasping and slicing jaws, and a quarter inch long poisonous stinger that can kill humans–is a malevolent marvel of evolution. It is ferocious and a voracious eater. It eats introduced European honeybees and relatively docile wasps. A single giant hornet scout finds a nest and marks the nest with a pheromone. The scout’s nest mates then descend on the honeybee nest and twenty to thirty of them slaughter 30,000 bees at the rate of 40 per minute until every bee is dead. Then the giant hornets eat every drop of honey in the hive and take the bee grubs back to their own nest and feed them to their ravenous offspring. The honeybees, having never encountered such powerful predators are defenseless.

However, Japanese honeybees have been subjected to the Asian giant hornet predation for a considerable period of time and have adapted admirably to the threat. Evolution provided a highly successful answer to the alternative of being devoured. The Japanese bees react to the scout wasp as soon as it arrives at their hive. The bees lure the scout inside their hive then swarm all over and around the wasp. Other hundreds of bees block the entrance. The wasp becomes covered in a tight ball of living bees which vibrate their abdomens, quickly elevating the temperature inside the ball and around the wasp to 117º F. The bees tolerate that temperature without difficulty, but the wasp cannot and is cooked to death before it can spread the information about the bees back to its nestmates. Unlike the European honeybees which evolved in an environment lacking giant hornets and are defenseless, Japanese honeybees lived for a long time with the predatory giant hornets and adapted to have an ingenious defense. The Japanese honeybees adapted and live; the European honeybees must adapt or die. That is the way of evolution—“Nature red with tooth and claw”, as Tennyson described.

ii.           ~Birds and larger insects eat katydids but do not eat rotten vegetation. Some katydids, however, have adapted a phenotype that mimics leaf patterns complete with rotten holes appearing on them. Over time, the mimicry became so exact and precise, that the katydids are difficult to pick out from a patch of real vegetation. The katydids’ natural predators are fooled, at least sufficiently to allow a goodly proportion of the katydids to escape predation and to live and procreate. Over vast periods of time and in tiny increments, the genes of the katydid survivors came to produce the faux leaf phenotype. This is the essence of evolution by the process of selection.

iii.          ~Common oldfield mice (Peromyscuspolionotus) burrow in dark brown soils. They have brown coats. A few such mice have varying degrees of lighter color in their coats. Hawks, herons, and owls hunt for the mice and, in the dark soil habitats selectively capture the lighter coated mice, and significantly more of the dark mice survive. However, in the white sand beaches ofFlorida, there are oldfield mice that are white. The same hunters fail to succeed sufficiently in their attacks on the mice that the colony survives in a healthy balance with its predators. Scientists performed an experiment with mice with multiple different color shades and patterns. The scientists isolated mice of different colors in an equal mix on habitats of dark and on habitats of light soil. They then released very hungry owls into the separate areas of habitat. The findings were as expected. The dark mice in the light colored soil habitat were decimated. The light colored mice on the light colored soil habitat survived and vice versa. The more the mouse color blended with the environment, the greater was the survival of that color of mice. The adaptive process was quite rapidly translated into selection and evolution with the color of the mice in the given habitat adapting over a few generations to the protective coloration in the majority. This evolutionary process was evident and persistent within a few hundred generations of mice, which are short enough, that the scientists could visualize the process during the period of their experiment (and not in a huge geologic time frame). In nature, the adaptive evolutionary process occurred about 6,000 years ago.

This heritability requires changes in genes—mutations. Other scientists working with the same strain of mice isolated two genes that have been involved in the dark/light adaptive transitions: Agouti, which is responsible for the dark color of some domestic cats and McIr, which is responsible for the productions of skin freckles and red hair, which mutation and trait is seen in abundance in the Irish. Obviously, the mutation–when it occurs–must allow the adaptive trait–in this case hair color–to be heritable, i.e., the mutation must not be lethal or cause the possessor of the mutation to be sterile. In the case of these mice, the mutation was benign.

            Many adaptations observed by either scientists or lay people are relatively direct, simple, and observable during the lifetime of the observers like those described above; but the same processes of random mutation, natural selection, genetic plasticity and heritability, and adaptation have worked over eons of time to produce the fascinatingly complex flagellum of e-coli, the delicate wing feathers of birds, and the host of intricate eyes seen in nature. No magic, no sudden creation of something from nothing, just a natural process—one that is well studied and understood by science.

2. Biogeography: There are three islands in the Juan Fernández group, which lies 400 miles west of Chili. They are among the most isolated of all locations on earth and; as such, they are considered an international treasure as a laboratory for the study of evolutionary change. One of the islands, Más a Tierra, is now called AlejandroSelkirkIsland, after the famous mariner who was marooned on the island at his own request and after four and a half years of isolation, became the real life model for the book, Robinson Crusoe. Besides Selkirk himself, the only mammals were goats, rats, and cats introduced by other sailors. Otherwise, the vast majority of the plants and animals are endemic to the island—i.e., they are present nowhere else on the planet. Those unique animals and plants include five species of birds—such as a giant rust-brown hummingbird, and the endangered Juan Fernándezfirecrown—126 species of plants including bizarre members of the sunflower family, a unique fur seal, and a handful of insects. There are more endemic species on the island than anywhere comparable. The truly remarkable finding is that there are no amphibian, reptile, or mammal species at all.

            In fact, the same classes of animals and fresh water fish are missing on all oceanic islands–land masses that came up out of the sea de novo–because of the great difficulty for those land-based animals to get there. Air and sea borne animals can get there as established by myriads of studies and experiments. Amphibians, reptiles, mammals, and fresh water fish are found in abundance on continentalislands–land masses that broke off from continents–because they were there from the beginning. Especially on oceanic islands, transport of animals is a relatively rare occurrence accounting for the very few mammals such as flying bats which do get there. Although some nonflying insects raft to oceanic islands or are carried there by birds or wind, most oceanic island insects are fliers, and most plants and animals and their fossils are most similar to those found on the nearest land masses despite the common finding of marked differences in environments in the two locations. The few species that do make it out to oceanic islands adapt and thrive in the new environment, and undergo speciation in remarkable numbers, e.g., Darwin’s finches; the Juan Fernández woody, treelike sun flower; and the few primates that made it to Madagascar 60 MYA and developed 75 different endemic species there over time. This thesis of the “Robinson Crusoe effect” is borne out powerfully by following the evidence of fossils and gene changes that comes from the study of evolution:

            Fossil seashells are found on mountain tops around the world. All native mammals inAustraliaare marsupials while almost all mammals elsewhere are placentals. These biogeographical oddities depend on three things: dispersal followed by evolution and then a changing earth. In addition, there had to be convergent evolution—different routes of evolution to achieve the same, or what is apparently the same, visible result, e.g., different flightless birds on multiple continents and animals such as marsupial moles inAustraliaand moles inAmericawith different genetic constructs which could not possibly have happened from dispersal alone. On the other hand, there are some plants and animals that are endemic to widely separated earthly locations and are the same or extremely similar: skunk cabbage, magnolias, and tulip trees, wild pigs and monkeys, European red deer and North American elk, which can only be explained by having lived in the same areas before continents separated and began their evolution after the separation.

            A prime example, and one which was predicted by evolutionary theory, is the study of fossil marsupials. The earliest marsupial fossils are found inNorth Americaand as time passed, they moved southward. Marsupial fossils dated to 35-40 MYA are found on the tip ofSouth America. The theory of continental separations predicts that fossil marsupials should be found on Antarctica with the same geologic time frame; the two continents separated about 35-40 million years ago. That could only have happened hadAustraliaandAntarcticaseparated carrying the same marsupials away toAntarctica. Indeed such fossils were found there as predicted. In brief, the only explanations which make any sense for the examples given above lie in the principles of evolution. Creationism is stumped by these biogeographicaloddities, and the subject is all but absent from creationism literature.

            One would expect fossil remains of specific animal strains to be found on the same continents upon which they live today, and that is the regular finding. The co-occurrence of fossils and modern animals lies at the biogeographical base for the evidence of an African origin for Homo sapiens and that species’ dispersal throughout the world. Extinct ape fossils and modern living apes inhabitAfrica, and the earliest human progenitor fossil forms are found there. Very few scientists doubt the very early origins of human-like creatures (~6-7 MYA) or that they began in southernAfrica.

3. Chromosome: In most sexually reproducing organisms, chromosomes occur in pairs, with one member of the pair inherited from each parent, and the two chromosomes are strongly bonded between the pairs of bases on opposite stands. The sequence of nucleotides in DNA can change from one generation to the next because of mutations—to beneficial, or to harmful, or to neutral traits. Beneficial traits often result in new DNA being spread within a population over multiple generations. Both neutral and beneficial mutations leave a record in DNA which can be seen in chromosomes. By comparing the DNA sequences of two organisms, biologists can see the genetic changes that have occurred since those organisms shared a common ancestor. For example, one of the most studied is the cystic fibrosis gene found in humans and is almost identical to a gene found in chimpanzees. Another is the gene that forms leptin which is involved in the metabolism of fats. There are only 5 differences between the two species in the 250 nucleotides that make up that gene in each species.

4. Co-Evolution:There are two fundamental kinds of processes or series of environmental stressors coupled with genetic changes involving more than one organism or gene that result in actions, changes, or change of function that bring about an evolutionary result:

i. Co-adapted genotypes. A gene has a particular effect that it causes only if there exists a structure upon which to work. Obviously a gene that causes wiring up of the brain in the developing embryo cannot work if there is no brain. These co-adaptations are built into the existing embryological process; and they may be determined, changed, deleted, or activated by genes. The gene’s environment is all the other genes in the body, and the genes persist in the cells of each successive individual body.

An interesting example of the adaptation process was found by Professor Charles Clarke and his colleagues at the Royal Roads University in Canada. They reported the discovery of a large, carnivorous pitcher plant in the Philippine Highlands which had evolved an alternative strategy from that of the same plant located inBorneo. TheBorneoplant eats insects and spiders, and the Philippine counterpart prefers that diet but where those are in short supply, the pitchers have grown to a size that accommodates an alternative source of crucial nitrogen. Over time, these pitchers have added a feature that allows them to produce copious amounts of nectar which attracts the tiny mouse-like tree shrew to harvest the nectar. The shrews, trapped inside the plant, leave nitrogen rich droppings directly on the precise spot where the pitcher plant can consume them and thereby survive until its preferred source of nutrition–insects and spiders–increase in sufficient supply to fulfill the needs of the plant.

ii. Arms-race. The complex interplay over time between predator and prey species–mortal enemies–results in changes linked to survival or extinction, both elements of evolution. Every morning on theSerengeti Plain, a Gazelle wakes up early and begins to run. In order to survive, the Gazelle must run faster than the fastest lion, or it will be caught and eaten.

            Every morning in the same area, a lion awakens and begins to run. He or she must be able to outmaneuver and outrun the slowest Gazelle, or the lion will use up too much energy on failures. If there are too many failures, the lion will starve. Each of the paired prey and predator species evolves incremental features that enhance survival.In this case, a significant part of the environment is the other animal and its innate capabilities. Mutations occur and a fraction of the Gazelles develop longer legs and can run faster. The lions which cannot catch the new generation of Gazelles die out, but among the population of lions are a few who are bigger, stronger, fleeter, have longer endurance, and have a greater proportional hunting success. They alone do not starve and live to pass on their beneficial genes. The Gazelles who are to survive the predation of these stronger, faster lions must themselves become still quicker, have faster reactivity, be more agile, have more endurance, and have keener senses of smell, hearing, and sight. And the lions facing the better adapted Gazelles live only if they come from a genetic population with greater ability to cooperate with other members of the pride in the hunting process, and on, and on, in an inexorable escalating stalemate.

            Cheetahs catch prey 70% of their predatory attempts, lions 50%. 3-5 million years of evolution provided cheetahs with a streamlined body that can achieve strides that carry them 23 feet on average. However, that streamlining came at a price: they lack bulky powerful muscles, jaws, or teeth; they are not able to fight well. 90% of their cubs succumb to predation and 50% of their food is stolen by more aggressive predators like lions and hyenas. They are quick but lack endurance and often cannot run long enough to catch their intended Gazelle or to evade the lion chasing them. 500 MYA the common ancestor of cheetahs, sail fish, and peregrine falcons evolved for speed, and its subsequent branches became the fastest animals in their differing environments.

            The genus Lepidoptera—butterflies and moths—provides an especially clear example of the arms race in action. Lepidoptera metamorphose from larva→pupa→adult. The first phase of life is spent as a caterpillar whose sole reason for being, for practical purposes, is to accumulate enough food and energy to complete pupation, making it little more than an eating machine. Caterpillars generally feed on only one or two plant species. In the rain forest, they must specialize because most rain forest plants produce toxic, sticky, or indigestible substances which deter herbivorous insects. In order to avoid starvation, the caterpillar has had to evolve counter measures by producing a veritable army of toxin neutralizing enzymes. The problem for the caterpillar is that the production of such large amounts of proteins is a highly expensive activity from the aspect of energy production. Hence, the caterpillar must conserve on the amount of enzymes it can make. The trade-off is that the caterpillar can only produce enough enzymes to neutralize the defenses of a few different plants. As one plant type evolves greater defenses, the caterpillar must produce more and more enzymes to deal with the defenses of just that one plant leaving little left over energy to deal with different plants. Inevitably, the caterpillar must evolve to become increasingly more specialized to be able to feed on just one or two plants. Such runaway co-evolution is known to be an important speciation producing mechanism.

            But the arms race for Lepidoptera is more complicated. As the caterpillar eats plants out in the open, it leaves evidence of its energy consuming activities. These evidences come to the attention of birds or other predators. Then begins a second co-evolutionary arms race. The predator must find ways to overcome the defenses of the caterpillar, and the caterpillar must evolve to avoid becoming a meal and for the species to avoid extinction. Lepidoptera has evolved two basic defense strategies.

            Deception or mimicry is one method. The caterpillar and other mimicking species evolve in a way that makes them appear to be a copy of some natural object, such as a twig, or eyes or other parts of larger and more dangerous creatures. One species of moth caterpillar resembles the whole head of a snake complete with a wiggling tongue appendage. Another looks like a bird dropping.

            In order not to starve, the predators in this co-evolutionary duel must evolve the ability to identify better and better the caterpillars’ deceptions. The caterpillar must become more and more like the object it mimics—better and better at camouflage. It is an eternal battle between species in a deadly interplay with life and death consequences and ultimately, species extinction as the result of failure in the arms race.

            Another strategy employed by caterpillars is to use poison and bright identifying colors. Often they acquire their toxins from their host plants. Rather than starve, the predators evolve ways to deal with poisons; so, in turn, the caterpillars become even more poisonous. This adds a complicated and sophisticated chemical warfare aspect to the co-evolutionary arms race. When the energy requirements to make toxins become overburdensome, some caterpillars evolve mimicry of still more toxic caterpillars to avoid predation (discovered by Henry Walter Bates during his investigations of moths and butterflies in the rain forests ofBrazil—BatesianMimicry).

            The examples of co-evolution among prey and predators seem nearly infinite. An extra pair of eyes, even phony ones, can be a boon to insects hunted by predators that target by sight. A saw-noses plant hopper’s first defense is camouflage. But if a bird, lizard, or other hunter takes aim, the insect can startle its foe by unveiling red spots that could be mistaken for the eyes of a larger animal. A butterfly pupa–a species discovered in Costa Rica by Daniel Janzen of the University of Pennsylvania–also shows a false face. “Peering” from a rolled-leaf shelter, its eyespots may deter small birds exploring the foliage for insect prey. Though a prevalent ploy in nature, the fake-eye look is not fool-proof. Animals that get caught may have secondary defenses, like a foul taste or toxic secretion. The plant hopper takes a more spirited approach, buzzing like a stinging wasp to provoke a quick release.

            The Hyalymenus nymph hides in plain sight. It has evolved to look and act like sap-eating ants, much fiercer creatures that can sting or wield toxins, spines, and communal grit. Predators that learn to avoid the ants are likely to bypass this imposter. At times the ants discover the copycat among them and attack Hyalymenus. Both ants and Hyalymenus are in a constant state of evolutionary flux in order for their species to survive.

            Moths and bats have a similar arms race. Bats emit sonic clicks to detect the movement of aerial insects at night. Some poisonous moths emit warning clicks to announce their lack of palatability. Nonpoisonous moths have tiny hairs that detect the slight air vibrations generated by the bat’s click, and the moth instantly drops beyond the bat’s flight path. As a consequence, over time, bats’ ears have become larger and more sensitive; and they have become more capable of rapid direction changes in flight. The moths have become more and more alert to the presence of bats and more and more capable of lightening quick and erratic movements. There appears to be no predictable end to this complicated dance macabre of nature.

Other examples abound in the natural world: Cows are the enemies of grass; short trees must increase in height to compete with taller trees or lose out, and this drives the average height up and up in the canopy. The coevolution of diet and other factors plays a role in the evolutionary arms race. An interesting example is found in Barlow, A., et. al., Co-evolution of Diet and Prey-Specific Venom Activity Supports the Role of Selection in Snake Venom Evolution. Proceedings of the Royal Society (Biological Sciences) 276: 2443-2449, July 7, 2009.

            Biologist Leigh Van Valen called this the ‘Red Queen Effect’ alluding to Lewis Carroll’sbook, Through the Looking Glass, where the Red Queen seizedAlice by the hand and dragged her faster and faster on a frenzied run through the countryside. No matter how fast they ran, the Red Queen and Alice always stayed in the same place. ToAlice’s complaint that in her country when you run fast you get someplace, the Red Queen replied, “Now, here, you see, it takes all the running you can do to keep in the same place. If you want to get somewhere else, you must run twice as fast as that.” The arms race produces bigger, better, faster, more cunning, more enduring, better adapted predators and prey species—the essence of evolution.

Evolution Blogspot 2. (Working Definitions, Part I.)

A little girl asked her mother, “How did the human race appear?” Her mother answered, “God made Adam and Eve, and they had children, and so all mankind was made.” Two days later the girl asked her father the same question. Her father answered, “Many years ago there were monkeys from which the human race evolved.” The confused girl returned to her mother and said, “Mom, how is it possible that you told me the human race was created by God, and Dad said they developed from monkeys?” The mother replied sweetly, “Well, dear, it is very simple. I told you about my side of the family, and your father told you about his.”

            It is the aim of the author [C.D.] to discuss biological evolution with goal of introducing, explaining, and clarifying this crucially important field of interest and education. Even before writing the first word, it is humbling to realize that it is impossible to be complete, or even comprehensive, about any single field involved with evolution, let alone the whole subject. I am certainly not so arrogant as to put myself forward as a font of all knowledge on the subject or even as an expert. Evolutionary literature is more than 150 years old, and there are millions of publications on the scientific study of how life began, flourished, became extinct, and evolved again to the marvelously complex, beautiful, and fascinating world in which we live.

            Let us begin with some well-recognized definitions related to evolution to form a basis upon which to discuss the processes—the “what” and the “how”—of biological evolution: 

Adaptation:A feature or phenotype or trait that evolved to serve a particular function or purpose.

Allele:Any of several forms of a gene, usually arising through mutation, that are responsible for hereditary variation.

Bauplan: A set of ancestral characters shared by all organisms (or one of their organs, e.g. the brain) forming a given taxon. The Bauplan, or body plan, is a relatively simple primeval genetic/embryological plan related to crucial, highly conserved genes which determines fundamental underlying similarities in phenotype that permits tinkering by genes to produce such disparate structures as fins, wings, and hands that nonetheless maintain the core form of the underlying ancient plan.

Chromosome: A long double stranded DNA molecule in a cell that contains a series of specific genes, located at their own intervals, along its length. The building blocks of the chromosomal strands are made of arrangements of four nucleotides, adenine, guanine, cytosine, and thymine, with each nucleotide having one of the basic chemicals.

Co-evolution: Two processes, including those occurring in different, even competing species, which interplay to effect a build-up of complexity and enhanced survivability.

Common Ancestor: an organism preceding in time and DNA commonality between two or more species.

Conservation of genes and proteins: In molecular evolutionary terms, conservation indicates perseverance of genes and proteins across evolutionary time and despite morphological changes in descendants.

Convergent Evolution: Similarity of structure or function due to independent evolution from different ancestral conditions—the appearance of apparently similar structures in organisms from different lines of evolutionary descent and by different processes at separate points in time; the independent evolution of similar structures or functions from non-homologous ancestral precursors.

Creation: The act of producing or causing to exist, engendering; the fact of being created. The Creation—the original bringing into existence of the universe and all of its components and inhabitants by God including the earth and the universe and all of the creatures therein. This is the common Judeo-Christian and Islamic doctrine that God, the Creator, produces something out of nothing, especially the human soul. There are hundreds of thousands of other Creation myths in addition.

Creationism, Intelligent Design: The religious doctrine that matter and all things were created substantially as they now exist a relatively short time ago (less than 10,000 years ago) and over a short period of time (6 days) by an omnipotent Creator as opposed to the concept that creatures gradually changed or evolved into their present state. This concept includes a literal acceptance of the biblical or other religious writings of the story of the creation of the universe, the earth, and all creatures at a given point in time and in the state in which they currently exist, as a factual depiction of actual history. This doctrine holds, among other arguments, that evolution is false because of irreducible complexity in nature—complex structures such as the eye, bacterial flagellae, or a hormone and its receptor, could not have developed separately andhave combined by chance. Only Creationism, or its updated synonym, Intelligent Design, can explain such complex and orderly structures and functions.

Creation Science: A Christian Protestant (Henry M. Morris and T. Robert Ingram) concept of Creationism developed in the 1960s that advocates a specific format of opposition to the scientific Darwinian Theory of Evolution. This doctrine of Creationism holds that the Creator God produced all things living and inanimate by supernatural means and relatively recently—on the order of 6000 years ago (The Biblical Book of Genesis, around 4004 BCE) and further holds that there is a body of scientific evidence that validates that premise.

Desoxy or Deoxyribonucleic acid (DNA): a biological molecule in the shape of a double helix, discovered by Watson and Crick (Watson, J.D., and Crick, F.H.C., A Structure for Deoxyribose Nucleic Acid, Nature 171:737-738, 1953) composed of chemical subunits known as nucleotides strung together in long chains. The sequences of nucleotides contain the information that cells require in order to grow, to divide into daughter cells, and to manufacture new proteins.

Encephalization: In comparative biology, the termencephalization describes the difference between animals in the amount of neurons available beyond the average determined by allometric body design. In Paleoanthropology, it designates the observed increase over evolutionary time in the absolute and relative size of the brain in hominids. In neuroanatomy, it describes the increased importance that higher brain structures play over lower ones such as are found in birds and mammals compared to other vertebrates and invertebrates.

Epigenetic: Changes in the phenotype that are not the direct result of alterations to the DNA sequence. These changes may result from chemical, traumatic, or mutational changes in proteins adjacent to genes. For example, changes to the phenotype of the brain may result from alterations to the body, rather than from changes in some expression in the central nervous system. Nuclear, chromosomal DNA is far more significant in heredity and evolution.

Evolution: Any process of formation, growth, or development—change—in the gene pool of a population from generation to generation by such processes as mutation, natural selection, phylogenetic speciation branching, genetic drift and combinations of those processes. Evolution is a core concept of biology that is based on the scientific study of past life forms, on the study of the relatedness and diversity of present-day organisms, and on the study of present and past genes and chromosomes. Adaptive evolution occurs largely by the successive accumulation of minor variations in phenotype—the visible characteristics of the organism.

Evolutionary Developmental Biology, Evo-Devo: A modern synthesis science that combines embryology (development), Mendelian genetics, molecular biology (genomics), and paleontology. It is, at its core, the study of genes and the rules and processes that shape animal form, especially during embryology, and the changes in genes that change that form during evolution. All animals presently on earth and all those lost in the mists of the past are products of two processes: development and evolution; eggs influenced by genes and changes over time by mutations affecting eggs—ontology recapitulating phylogeny and over eons changing both. With the discovery of DNA, chromosomes, genes, “tool-kit” genes, the genetic code for genes which produce vital proteins, and gene switches (regulatory DNA), further research proved that all animals share a small number of basic genes that have been altered to produce the incredible diversity of the plant and animal kingdoms that we see in all of its beauty and complexity resulting from old genes developing new tricks.

Fact: Something that actually and provably exists; reality, a truth. A fact in science is an established observation or measurement or other form of evidence that can be expected to occur the same way every time under similar circumstances. Fact is also established by an accumulation of testing and confirmation by repeated experimentation and verification by actual experience until its validity is no longer in question, no longer in doubt. No new evidence is expected to demonstrate that the earth does not orbit around the sun or that matter is not composed of atoms.

Evolution is such a concept. It is the truth. No longer do scientists work to prove whether or not evolution is valid; rather, they concentrate their efforts on how the process works in a specific situation and what predictions can be made based on the principles of evolution. Scientists are confident that the basic components of the theory will not be overturned by new evidence. Like all theories, facts are expected to be accumulated which will produce continuing clarification and refinement of details.

Gene: The basic unit of heredity; a segment of DNA sequence located at a defined interval on a chromosome. Genes are the regions on the DNA that carry the instructions for making proteins.

Genus: a grouping of related animals or plants—the major subdivision of a family or subfamily in the classification of organisms, usually consisting of more than one species.

Homeodomain: A 180 base pair, 60 amino acid, part of proteins that corresponds to the homeobox genes that are involved in the regulation of the development (morphogenesis) of animals, fungi, and plants. A homeobox gene is able to bind to DNA and therefore can act as a transcription factor.

Hominid:Humans and African Apes—the taxonomic family of man.

Hominin:Humans

Homology:Homology (Greek-agreement) is a likeness between animals–similar characteristics in two animals that are a product of descent from a common ancestor rather than a product of a similar environment. It is the relationship between two or more characteristics that were continuously present since their origin in a shared ancestor.

Hox Genes:homeotic box or homeodomain transcription factor genes, Hox for short, which cluster together in short assemblages of amino acid sequences on segments of chromosomes to produce specific changes in development and post-birth function. Important developmental regulatory genes involved in specifying positional information along animal body axes, including appendages. They confer segmental identities

Hypothesis: A proposition or set of propositions set forth as an explanation for the occurrence of some specified group of phenomena. An hypothesis may be asserted merely as a provisional conjecture to guide investigation as in a working hypothesis or accepted as highly probable in view of the accumulation of established facts. In science a hypothesis is customarily regarded as a conditional proposition, beyond a mere guess or new assumption, but less valid or well established than a theory.

Law: In science or philosophy, a law is a statement of a relation or sequence of phenomena invariable under the same conditions such as a mathematical rule.

Mutation: A change in the sequence of nucleotides in DNA. Such changes can alter the structure of proteins or the regulation of protein production and thereby may alter the function of proteins, nucleotides, genes, chromosomes, and eventually inheritance of biological characteristics which may allow a favorable response to an environmental stress that leads to natural selection and improved survival. That improved survival leads to increased progeny with the same inherited qualities. Most mutations, however, are either neutral (of no effect) or lethal.

Natural Selection: Differential survival and enhanced successful reproduction of organisms as a consequence of response to the characteristics of the environment.

Parsimony: A principle of scientific inquiry that one should not increase beyond what is necessary the number of entities required to explain anything.

Phylogenetic Tree: A genealogical map of interrelationships among species, with a measure of relative or absolute time on one axis. It is also called a tree-of-life or a phylogeny.

Population Genetics: The branch of genetics study concerned with the hereditary makeup of groups or populations, usually relatively similar and related groupings.

Science: A branch of knowledge and/or study dealing with a body of facts or truths systematically arranged and showing the operation of general laws such as the mathematical sciences. Science involves developing systematic knowledge of the natural physical, material, and chemical world gained from observation and experimentation which is subject to review and revision to accommodate new or additional factual information. Science is based on a sound theoretical basis with an accumulation of empirical and experimental data obtained from the natural and sensory world rather than from feelings, intuition, revelation, or the supernatural.

The Scientific Method: The use of evidence to construct testable explanations and predictions of natural phenomena as well as the knowledge generated through this process. Science is, therefore, a method of research in which a problem is identified, and relevant data is gathered by as precise methods as are available; an hypothesis is formulated based on these data; and the hypothesis is tested until enough data is accumulated and contrarian views are disproved to warrant the more advancedstatus of being a theory.

Scientism: The belief that the assumptions, methods of research, and methodology of the physical and biological sciences are equally appropriate to and essential for all other disciplines of human activity such as the humanities, religion, and the social sciences. Self-appointed successors toDarwinhave been tempted to see evolution by natural selection as a universal phenomenon rather than a narrow biological theory. Evolution has been applied to the changing of the universe, historical changes of human civilizations, interactions among societies, and to petty considerations of clothing and hair style.

Such thinking involves an over emphasized analogy and an excess of excitement about even a tenuous analogy. This usually represents an exaggeration of the applicability of the scientific method and is suggestive of pseudoscience. Strictly speaking–by its very definition and nature–science cannot address processes or beliefs that do not depend on empirical evidence or natural phenomena and do depend on concepts of the supernatural. Science flourishes in an atmosphere of doubt and challenge, refutation, innovation, and change; religions are not particularly receptive to doubt, challenges to authority, or to change. Supernatural entities cannot be investigated by the scientific method. Science has nothing to work with regarding elements of the supernatural. Science and religion are separate belief systems and address aspects of human understanding in different–and largely mutually exclusive–ways. Evolutionary science is most successful and precise if it is limited to biological (rather than social) events in the natural world. For the most part, it is well for scientists to resist using analogies except in the simplest way with a disclaimer that the analogy is not science, but only a means of illuminating a concept.

Sexual Selection: A subset of natural selection which operates in such a way as to increase an individual’s chance to find an accepting mate and to procreate. Sexually selected traits evolve and persist if they more than offset the male’s diminished survival with an increase in his survival. The most obvious example of a great many is the peacock’s tail. It must be replaced each year, requires an exorbitant amount of energy, and makes the peacock an obvious target for predators. However, peahens preferentially select the most flamboyant peacocks for mating, and the reproductive rate of such males more than fully offsets their deaths by predation. In addition to this female preference–which enhances a particular male’s chances–is the male vs. male direct competition. The largest or most ferocious or most determined male wins the female by establishing to her that he is the fittest or by the simple expedient of driving off other suitors. A prime example is the great battles among huge elephant seal males that leave one alpha male to control a large harem of smaller females once they come ashore.

            Closely intertwined with sexual selection is sexual dimorphism—the difference in form, often a striking difference–between the two sexes with the more elaborate traits almost always belonging to the male.

Species: A group of interbreeding natural populations which are reproductively isolated from other such groups. (Ernst Mayr). The biological species is the unit of evolution.

Speciation: the establishment of an entirely new and reproductively separate species, is the only process of adaptation that produces a split into two separate lineages that do not interbreed with one another—reproductive isolation.

Theory: In every day parlance, a theory is a hunch, a speculation, or a proposed explanation whose status is still conjectural compared to other, better established propositions that are considered to be matters of fact. Opponents of the Theory of Evolution trivialize the foremost basis of the understanding of biology by referring to it as “only a theory”. However, by strict definition, a scientific theory is a coherent and well documented and establishedset of generalized propositions used as principles of explanation of a class of phenomena.

The Darwinian Theory of Evolution by Natural Selection: Darwin’s theory of natural selection entails two main aspects, namely, that:

1. organisms produce offspring with at least some heritable variation, and,
2. that organisms generally produce more offspring than their environment is able to sustain.

            At its simplest, Darwin’s theory, with the refinements of 150 years of study, includes, even requires, six basic components:

1. Evolution
2. Gradualism
3. Speciation
4. Common ancestry
5. Natural selection
6. Nonselective mechanisms of evolutionary change

            Given these two fundamental aspects and the six basic components, some variants are necessarily fitter than others in the sense that their offspring are more likely to survive in an environment and from environmental changes and produce a next generation of offspring. It follows that a species undergoes genetic change over time. Darwin proposed that such changes were generally small, sporadic, incremental, and required extremely long periods of time to manifest themselves for the most part—a process labeled gradualism. The result is the development of new species by splitting—speciation. Looking in reverse, the development of new species implies that there was an ancestral species, a single or few common ancestors. Darwin’s most remarkable contribution to the world of natural science and to biology, and certainly his most controversial idea, was the concept of natural selection. That concept gives a purely materialistic explanation of what otherwise appears to be explainable only by invoking a Creator or Intelligent Designer, a nonscientific postulation. At its simplest, natural selection acts on populations with the capacity to alter their genetic makeup and thereby to reproduce more successfully in a given environment. Reproductive capacity is the key to natural selection and to evolution. There are other, more minor, contributors to evolution than natural selection. The “environment” may by internal, for example. A family, or a population, may simply produce more offspring than another by having more gene material or genes that favor a shorter gestation time and more offspring per parturition. In this instance, the genetic changes may be more random than an adaptation to an environment. This genetic drift plays a relatively minor role in the evolution of small populations.

Vestigiality:(From the American Heritage Science Dictionary). Relating to a body part that has become small and has lost its use because of evolutionary change. Vestigial characters are homologous anatomical parts, behaviors, and biochemical pathways of organisms which have lost all or most of their original function. Some disappear in early embryonic development and only rarely are manifested in adults. On a microscopic level, there are myriads of vestigial or relic DNA or protein material in the genome of all organisms as a result of failure of the results of some mutational products to prevail, but remain trapped in the genomes as evolutionary genetic fossils or ghosts.

Williston’s Law: Named for Samuel Williston, an eminent Harvard legal scholar, who viewed the law as being a body of scientific rules from which legal decisions may be readily deduced; i.e. existing rules are self-evident truths. Williston concluded that a law must be stated as simply as possible. In terms of evolution, as defined by Sean B. Carroll–a molecular geneticist–Williston’s Law can also be seen as a statement of the trend over the course of vertebrate evolution to reduce the number of components in specific body parts. This relates to the Hox gene family which creates a molecular blue-print for the body pattern, a Bauplan, and plays a major role in the origin of new features without evolution having to require an entirely new structure (an statistically unlikely scenario) every time a change appears. Williston’s Law, as expressed in evolutionary terms incorporating Hox gene information, provides a fairly simple explanation for change from DNA to diversity as provided by the study of molecular genetics wedded to the evolution of naturally acquired animal design. The principle of genetic frugality and use and reuse of genes underlies the evidence that has been adduced to debunk the Intelligence Design proponents’ argument of irreducible complexity to attack evolution.

I first saw Jon McNaughton’s painting, One Nation Under God, in 2009 when it was just becoming popular. It was more than popular in the area where I live; it was important to people with rather strong conservative political opinions and with very negative opinions about science as it applies to humans and especially as it applies to biological evolution and very especially as it applies to the evolution of humans. Mr. McNaughton holds a BFA [Bachelor of Fine Arts] from BYU [Brigham Young University] and lives in Spanish Fork, Utah. By his own statement, he created the painting inspired by a vision he received during the 2008 elections which resulted in a shift to the left of which he disapproved. The painting depicts Jesus Christ surrounded by actual historical characters from American history, and symbolic characters who serve as archetypes:  On the left there are Satan, a liberal news reporter who obviously represents the distortion of news away from the religious and political right, a handicapped child, a smirking professor fondly turning the pages of Charles Darwin’s book, the Origin of the Species, a remorseful Supreme Court justice crying over his court’s Roe v. Wade decision with a pregnant woman hovering nearby in the corner set aside for Satan. On the good side of Christ are such notables as Ronald Reagan and James Madison, and archetypes including a noble farmer, a Christian minister, a U.S. Marine, a handicapped child, a black college student, a schoolteacher who has some resemblance to the former ultraconservative vice-presidential candidate, Sarah Palin, and a young white male who represents the rising generation who aspires to set things right.

McNaughton is a superb artist; his religious paintings are excellent and evocative. Any Christian home would feel comfortable and uplifted by hanging any one of them on the wall. The details in McNaughton’s works and the symbolism portrayed in them–and especially in One Nation Under God–are serious art. One Nation Under Godis more than that. It is a religious and political statement of opinion, an opinion shared by perhaps the majority of Americans. The United States is the world’s most religious country by many standards of comparison. On his web site, Mr. McNaughton speaks of the immigrant in the picture holding his hand in the air, “I wanted him to have a look of shock when he realizes where the source of America’s greatness comes from as he sees Christ holding the Constitution.” He goes on to make the following statement about the inclusion of Charles Darwin’s theory in the company of Satan. He says, “Yes, I have read the book and yes I do believe in many of the theories it espouses. What?! No, I don’t think the book should be burned and kicked out of the school curriculum. Some of the rebuttals I have heard in regard to this subject in my painting are unfounded. I believe that this book is a standard that the left uses to push Christianity out of the Educational Forum. I believe that we need faith in our schools. I believe that I did not evolve from an ape. You may disagree…”

I have no argument with Mr. McNaughton’s right to express his opinion both in his painting and in his words. However, I do have a concern about the concept that the theory of evolution is evil or somehow an anti-religious notion—“just a theory” as many right-wing opponents would tell you. Since Darwin published his book in 1859, a great many scholars and religious people have sought to disprove his assertions. No scientific evidence has ever been adduced that successfully challenged the theory. Multiple court battles launched by opponents have failed. The opposition to the theory of evolution has had to resort to publishing unfounded hypotheses which are unsupported by rigorous scientific evidence—the most recent being the Intelligent Design Theory. Worse, the opposition has been reduced to using inflammatory mocking rhetoric, artistic depictions evoking a sense of evil about the theory, and–more egregious–artistic caricatures. Since the theory was published in the world’s scientific literature, Charles Darwin has been portrayed as a tree-climbing anthropoid, as an ape sitting on a tree limb cuddling two apes—the latter caricature, a painting by a German artist on the occasion of Darwin’s one-hundredth birthday. Darwin has been portrayed as a monkey with Darwin’s head. He holds a mirror up to another monkey which is sitting next to him. One is led to the conclusion that the professor of biology is inviting the monkey to ponder about himself and his existence. When all else fails, all is not lost; one can still resort to name calling.

When I saw Mr. McNaughton’s painting—shown to me by an ardent admirer—I had the temerity to ask what the admirer knew about evolution. The answer then, and most of the time I ask it, is “It’s just a theory; the concept of man coming from a monkey is stupid.” The most emphatic argument I encounter is best described as the Fallacy of Personal Incredulity:“I don’t believe it; therefore, it is not true.” I concluded that these spurious arguments are examples of the certainty of ignorance. One is entitled to an opinion that differs from mine or anyone else’s, but mockery as the last resort of ignorance is hardly a compelling argument.

I would like to give a brief explanation of evolution in several subsequent blogspots because I think this concept is important, inflammatory, fascinating, and one of the fourpillars of biology—the natural world—along with the atomic theory, the cell theory, and the genetic theory of reproduction. If we are going to argue, at least we should know what the argument is about. Why should we fear knowledge?

“I believe in the dignity of labor whether with head or hand; that the world owes no man living, but that it owes every man an opportunity to make a living.”

-John D. Rockefeller, Jr.

“I believe in the sacredness of a promise, that a man’s word should be as good as his bond; that character—not wealth or power or position—is of supreme worth.”

-John D. Rockefeller, Jr.

“I believe the rendering of useful service is the common duty of mankind and that only in the purifying fire of sacrifice is the dross of selfishness consumed and the greatness of the human soul set free.”

-John D. Rockefeller, Jr.

“I believe that love is the greatest thing in the world; that it alone can overcome hate; that right can and will triumph over might.”

-John D. Rockefeller, Jr.

“Anyone who imagines that bliss is normal is going to waste a lot of time running around shouting that he’s been robbed. The fact is that most putts don’t drop; most beef is tough; most children grow up to be just people; most successful marriages require a high degree of mutual toleration; most jobs are often more dull than otherwise. Live is like an old-time rail journey…delays, side tracks, smoke, dust, cinders, and jolts, interspersed only occasionally by beautiful vistas and thrilling bursts of speed. The trick is to thank the Lord for letting you have the ride.”

-Gordon B. Hinckley, President of the Church of Jesus Christ of Latter-day Saints

“Go confidently in the direction of your dreams! Live the life you’ve imagined.”

-Henry David Thoreau

“Life—happy or unhappy, successful or unsuccessful—is extraordinarily interesting.”
-George Bernard Shaw

“Be glad of life because it gives you a chance to love and to work and to play and to look up at the stars.”

-Henry Van Dyke

“Collectively reinforced egocentric and sociocentric thought, conjoined with massive technical knowledge and power, are not the foundations for a genuine democracy.”

-Richard W. Paul, Critical Thinking: Fundamental to Education for a Free Society

“Open-mindedness may be proper, but it is not the ‘natural,’ disposition of the human mind.”

–Richard W. Paul, Critical Thinking: Fundamental to Education for a Free Society

“Ever notice how these days many women wear their stress like a badge of honor? In our culture, being busy has come to equal having high status Indeed, its actually embarrassing to admit that we have free time. Although most of us know that relaxing is beneficial, we simply can’t give ourselves permission to do so. One psychologist calls this ‘hurry sickness.’ We’re psychologically addicted to the idea that success equals busyness. And most people today live with high levels of stress hormones in their bodies; so, when they relax, they feel anxious. Women are especially prone to this anxiety. They’re under much more pressure to do everything well—be a good wife, a good mother, and employee. The bottom line is, taking time for yourself is essential—not only for you, but for all of the people close to you.”

-Sandi Shelton, Relax

“Take care of the luxury, and the necessities will take care of themselves.”

-Oscar Wilde

“When people agree with me, I always feel that I must be wrong.

-Oscar Wilde, the Critic as an Artist

“If I had two faces, would I be showing you this one?”

-Abraham Lincoln

“The first thing we have to do is to kill all the lawyers.”

-William Shakespeare, Henry VI

“No me daráspena y ninguno se entregarapor ti.”

-[No quarter asked, and none given.]

“They are able because they think they are able.”

-Virgil, The Aeneid

“A wise man knows everything; a shrewd one, everybody.

-Anonymous

“Heaven ne’er helps the men who will not act.”

-Sophocles

“America is a tune. It must be sung together.”

-Gerald Stanley Lee, Crowds

“This generation of Americans has a rendezvous with destiny.”

-Franklin Delano Roosevelt

“When angry, count four; when very angry, swear.”

-Samuel L. Clemens, Pudd’n head Wilson

“Beware the fury of a patient man.”

-Dryden, Absalom and Achitophel 

“No sensible person ever made an apology.”

-Ralph Waldo Emerson

“Wise men argue cause and fools decide them.”

-Anacharsis

“Fortune favors the audacious.”

-Desiderus Erasmus

Either you do not read newspapers, listen to the news, or watch television if you are not familiar with the Trayvon Martin homicide case in which the “stand-your-ground laws of Florida factored in significantly. Such laws give individuals the right to use deadly force, including the use of firearms, to defend themselves without any requirement to evade or retreat from a dangerous situation. In such situations, a person is justified in using deadly force, and the stand-your-ground law would be a defense or immunity to criminal charges and civil suit. In most states with sand-your-ground laws, limitations apply as to the situation. There may be a distinction about whether the concept applies only to defending lawfully occupied locations, which was not the case in the Martin case. States have differing approaches to the distinction between immunity and a defense. In general, an immunity bars civil suit, criminal charges, arrest and detention. A defense–on the other hand—is a fact or set of facts that may avoid or mitigate the adverse legal consequences of the defendant’s otherwise unlawful conduct. In some states this may be limited only to an affirmative defense—a concept applying to both civillawsuits and criminal charge. That defense is a fact or set of facts other than those alleged by the plaintiff or prosecutor which–if proven by the defendant–defeats or mitigates the legal consequences of the defendant’s conduct. In civil lawsuits, affirmative defenses include the statute of limitations, the statute of frauds, and waiver. In criminal prosecutions, examples of affirmative defenses are self-defense,insanity, and the statute of limitations.

Most states have some form of stand-your-ground law and many of them link those laws with castle doctrine described in BlogPosts 1-4 of this series. There is considerable difference among the states. Some have laws; some have assumed policies; some use case law; and some use definite legislation. Michigan’s law is clear but has some grey areas: MCL 780.972, provides that “[a]n individual who has not or is not engaged in the commission of a crime at the time he or she uses deadly force may use deadly force against another individual anywhere he or she has the legal right to be with no duty to retreat if . . . [t]he individual honestly and reasonably believes that the use of deadly force is necessary to prevent” the imminent death, great bodily harm, or sexual assault of himself or another individual. The grey area comes in the wording.  The “reasonable belief” requirement is different from a “sincere belief”, meaning that a “reasonable person” should be able to examine the situation and see a threat to life or serious injury. On the other end of the spectrum is California. California provides civil remedy to those who incur damages resulting from the use of self-help by a defender,and the CaliforniaSupreme Court has been critical of the doctrine since 1858. It is not difficult to understand that considerable controversy occurs whenever the issue arises in court, or in public debate wherever the subject is broached.

                How should reasonable people or a court view a person who is mugged at gunpoint then shoots the mugger in the back as he is running away? It could be argued that he person who was mugged might “sincerely” believe the mugger was going to turn around and shoot him or her. It could also be argued that such a defense is too subjective and not considered to be “reasonable” under the circumstances. George Zimmerman shot and killed Trayvon Martin—a stipulated fact in his trial in Florida. The jury acquittedZimmerman. The relevance of the stand-your-ground provision of the self-defense law to the Zimmerman case has been questioned and is controversial, political, and has racial overtones. The defense argument that carried the day was that Zimmerman claimed he was restrained at the time of the shooting and had no option to retreat. Although Zimmerman’s defense team did not use the “stand your ground” defense during their trial and instead opted to use “self-defense” as their official defense, Circuit Judge Debra Nelson’s instructions to the jury included the statement that he had no duty to retreat as per Florida’s stand-your-ground law. The Zimmerman/Martin case will be debated whenever issues of reasonableness, stand-your-ground, or self-defense arise.

                The concept of justifiable homicide in in common sense, criminal law, and civil action turns on the lines between excuse, justification, and exculpation; and many opinions and case outcomes are based on the thinker or the trier-of-fact’s interpretation of any or all of those considerations. A ruling of justifiable homicide in a criminal proceeding, it must objectivelyproved to a trier of fact—jury or judge– beyond all reasonable doubt, not just to a level of preponderance of evidence–that the defendant intended to commit violence. If that cannot be proved, a homicide in this instance is should be ruled blameless. There is a considerably less stringent set of criteria authorizing deadly force in stand-your- ground rulingsin states where they apply.The degree of response as matched to the degree of threat may be tested. If the level of force used in defense matches the force threatened. It is significant if the putative victor in a conflict first retreated or showed a clear intention not to fight but then was obligated to do so for self-preservation. This decision may hinge on questions of whether or not avoidance was possible in the time available. If true, the killer may be exculpated. Obviously, a victim who escapes may not return for revenge or to prevent future attacks.

                Obvious justification under the law throughout the United States and in most countries exists for killing by a combatant during an officially declared war, protection against external aggressors during incursions, police officers killing suspects in the line of duty, and judicial execution. There is a doctrine of necessitywhich allows–for example–a surgeon to separate conjoined twins, killing the weaker twin to save the other. Under certain circumstances, It may be necessary to abort a baby during labor if the mother’s life is threatened, but Roman Catholic doctrine takes the opposite view—sacrifice the mother. All of these instances constitute non-criminal homicide.  The United States and much of the world condones abortion as a “woman’s choice”, but American law across the board considers feticide to constitute a double murder whena pregnant woman is the victim of homicide—a rather schizophrenic approach to the death of unborn infants.

Several civilized countries—Belgium, the Netherlands and Luxembourg and not the United States–condone euthanasia in certain circumstances. Assisted suicide is homicide where the individual/patient has to make the decision and to take the final action themselves–unlike euthanasia where an another person kills to relieve suffering–is legal in Switzerland. There are assisted dying laws, for terminally ill mentally competent adults only, in the U.S. states of Oregon, Washington and Vermont.