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:
- organisms produce offspring with at least some heritable variation, and,
- 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:
- Evolution
- Gradualism
- Speciation
- Common ancestry
- Natural selection
- 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.