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:
- random genetic mutation (permanent transmissible changes to the DNA or RNA of a cell that inevitably occur at a certain rate in genes)
- 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%)
- 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
- 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.