Evolution

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Evolution and the Origin of Life  
Controversies That Have Divided America
 Evolution Crossword Puzzle 
© W.P. Armstrong 3 March 2012
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Table of Contents
  1.    Introduction: Evolution Defined
  2.    Is Evolution A Theory Or A Fact?
  3.    Evidence For Genetic Variability
  4.    The Origin Of Asexual Species
  5.    Evolution & Gene Duplication
  6.    Telomeres & End Replication Problem
  7.    Evolution & Irreducible Complexity
  8.    Scientific Theory vs. Common Theory
  9.    Moving Rocks: Theories or Hypotheses?
10.    K-T Boundary & Demise Of Dinosaurs
11.    Scientific Theory & Scientific Law
12.    Evolution Based On Fossils & Cladistics
13.    Monophyletic Groups (Duckweed Family)
14.    Coexistence Of Grasses & Dinosaurs
15.    Origin Of The First Land Plants On Earth
16.    Origin Of Flowering Plants: Angiosperms
17.    The Remarkable Angiosperm Life Cycle
18.    Adaptive Radiation: Hawaii & Galapagos   
19.    Homoplasy: Parallel & Convergent Evol.
20.    Homoplasy: Carrion Flowers Attract Flies   
21.    Origin Of Eyes In Distantly Related Animals
22.    Punctuated Equilibrium & Natural Selection
23.    Symbiogenesis: Genomic Mergers
24.    Coevolution Of Fig & Fig Wasp
25.    Vicarious Selection In Dioecious Figs
26.    Coevolution Between Acacia & Acacia Ant
27.    Hybridization Between Harvester Ants Spp.
28.    Selection & Survival Of The Fittest
29.    Selection in Tardigrades: Over-equipped?
30.    Faith & The Existence Of Coconut Pearls
31.    Propositions For The Origin Of Life
32.    Alkaline Vents & The Origin Of Life
33.    Danger Of Imposing Non-Science Dogma
34.    The Origin Of Life By Probability Alone
35.    Did Life Evolve From Common Ancestor?
36.    Origin Of Magnificent Grand Canyon
37.    True or False Summary Statements
38.    Literature Cited In This Report

Note: Paragraphs are numbered in small case
in order to communicate with reviewers.

    1. Introduction

  1. One of the problems in understanding evolution is that it may be defined in different ways. According to the Random House Webster's College Dictionary (1999), biological evolution is a change in the genetic makeup of a population from generation to generation. It may also be defined as the development of species or other groups of organisms (genera and families) from earlier forms by natural selection. Microevolution refers to changes at or below the species level, while macroevolution generally refers to large-scale changes over a long period of time resulting in new species. In this article I have attempted to clarify and summarize some of the major concepts and terms used by evolution scientists. Depending on the author, evolution may be referred to as a theory, hypothesis, law, truth, and fact. In fact, these terms are often used interchangeably and sometimes incorrectly, even by prestigious biologists. In my opinion, evolution is a well-established scientific theory supported by facts. For science teachers, I have included an extensive bibliography and a crossword puzzle containing many of the terms defined in this article.

  2. The noun evolution is derived from the verb evolve, meaning to gradually change with time. Evolution can be defined in several different ways. For example, Wayne's Word has evolved from a humorous, natural history newsletter sent out to friends, to a large on-line, hyperlinked, peer-reviewed textbook of natural history with millions of hits per month. Another definition is organic (biological) evolution that incorporates numerous facts and well-substantiated, tested hypotheses. It is usually associated with natural selection based on the original published work of Charles Darwin and Alfred Russel Wallace.

     Try The Wayne's Word Evolution Crossword Puzzle 


    2. Is Evolution a Theory or a Fact?

    Four Important Definitions Used In The Teaching Of Science:
    Working Group on Teaching Evolution, National Academy of Sciences (1998)

    1. Fact: In science, an observation that has been repeatedly confirmed.

    2. Law: A descriptive generalization about how some aspect of the natural world behaves under stated circumstances. Laws can be very useful in supporting hypotheses and theories, but like all elements of science they can be altered with new information and observations.

    3. Hypothesis: A testable statement about the natural world that can be used to build more complex inferences and explanations, such as a scientific theory.

    4. Theory: In science, a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses.

    It Is Obvious From The Following Quotations Regarding Evolution
    That The Terms Theory & Fact Are Used In Several Different Ways

  3. In November 2004, suburban Atlanta biology textbooks included a warning sticker that said:

      "This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered."

  4. On November 19, 2004, the Dover School Board of Pennsylvania passed a resolution requiring teachers to read a statement to students in 9th grade science classes endorsing intelligent design as an alternative explanation for the origin of life.

      "The Pennsylvania Academic Standards require students to learn about Darwin's Theory of Evolution and eventually to take a standardized test of which evolution is a part. Because Darwin's Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations. Intelligent Design is an explanation of the origin of life that differs from Darwin's view. The reference book, Of Pandas and People, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves. With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the Origins of Life to individual students and their families. As a Standards-driven district, class instruction focuses upon preparing students to achieve proficiency on Standards-based assessments."

  5. The resolution was challenged a year later in the United States federal courts: Case No. 04cv2688, "Tammy Kitzmiller, et al v Dover Area School District." The plaintiffs successfully argued that intelligent design is a form of creationism, and that the school board policy thus violated the Establishment Clause of the First Amendment to the United States Constitution.

  6. The argument whether evolution is a theory or a fact is an invalid comparison. Evolution is a scientific theory that has explained the factual evidence of scientists for more than a century. All interpretations of facts in science are provisional and subject to challenge. Under a strict definition, a scientific theory should not be called a "fact" even though it explains all known facts and has survived the test of time. There is always the possibility that a scientific theory will be updated or changed as new evidence is discovered. The theory of evolution assumes the existence of life and is directed to an explanation of how life evolved. It does not deal with the origin of life, and it does not presuppose the absence of a creator or God. Although the origin of life is often included in debates about evolution, it is a very different topic that does not have all the empirical evidence of biological evolution. Scientific explanations for the origin of life are more properly referred to as hypotheses rather than scientific theories. Intelligent design is a non-scientific argument or assertion that life "owes its origin to a master intellect." Please refer to Origin of Life later in this this discussion.

  7. According to E.C. Scott (Evolution vs. Creationism, Univ. of Calif. Press, 2004), most people consider facts more important than hypotheses, theories and laws. In fact, they rank these terms in order of importance as follows: Facts-Laws-Theories-Hypotheses. Scientists rank these terms in the following order from most important to least important: Theories-Laws-Hypotheses-Facts. Our interpretations of facts are certainly not set in stone and are often changed in science. Consider the number of chromosomes in a human somatic cell. In the 1950s the number was determined to be 48. This fact was published in all biology textbooks. With better techniques in staining chromosomes, the number was later revised to 46, 23 from each parent. Disagreement on chromosome numbers still occurs to this day, particularly with plant species containing numerous chromosomes that often overlap each other making accurate counts very difficult. For as long as I can remember, Pluto has been listed as the ninth planet in our solar system. Recent studies of its orbital patterns and other factors indicate that Pluto is not a true planet compared with Mercury, Venus, Earth, Mars, Jupiter, Saturn, Uranus and Neptune.

  8. The following image shows an example of a disputable interpretation of facts: The number of chromosomes in a species of Brodiaea from coastal southern California. The stained microscope slide is my factual evidence for the chromosome number of this species. My original count was 36; however, another botanist prepared his own microscope slides (factual evidence) and came up with 40+ chromosomes. In my original microscope slide, there may have been some smaller chromosomes that were obscurred by larger ones. Therefore, my orginal count of 36 may have been too low. My factual evidence (the prepared microscope slide and photo image) have not changed, but my interpretation of the factual evidence probably needs to be changed.

    Microsporogenesis in the San Marcos Coastal "BTK" showing the first division of a pollen mother cell (microsporocyte). Cytoplasmic division (cytokinesis) has not occurred yet. The two chromosome clusters (2 sets of chromosome doublets) contain at least 36 chromosomes, probably more depending on how you count overlapping chromosomes. There are very small chromosomes that are possibly obscured by the larger ones. [500 x]

  9. Another example of how our interpretation of tangible, factual evidence has changed is the fossil remains of a petrified fig syconium named Ficus ceratops. The 70 million-year-old Hell Creek Formation in the Montana badlands is rich in fossil fig syconia and dinosaur fossils, including Tyrannosaurus rex, Triceratops and the amazing duck-billed Hadrosaurus. In fact, Ficus ceratops is named after the dinoaur Triceratops. Recent excavations in T-rex fossil beds of Canada revealed that the so-called fig syconia were actually covered with spines. Our interpretation of these fossilized fruits has changed: It is now thought that they are from of an extinct palm named Spinifructus antiquus. See Section 10 (K-T Boundary & Demise Of Dinosaurs).
  10. There is compelling evidence to show that humans once had 24 pairs of chromosomes (2n = 48) like present-day great apes (orangutans, gorillas and chimpanzees). Like all other 23 chromosomes, chromosome #2 has a terminal genetic marker called a telomere. Telomeres shorten prior to chromosome replication and cell division. Shortened telomeres eventually signal the cell to stop dividing. In cancer cells, an enzyme called telomerase keeps telomeres at a constant length so that cancer cells keep on dividing over and over again. Chromosome #2 has a second telomere in the middle region, indicating that two chromosomes joined together end-to-end and became permanently fused into a single chromosome. The sister chromatids of a chromosome doublet are attached in a constricted region of the chromosome called the centromere. Each chromosome has a single centromere; however, chromosome #2 has two centromeres, further evidence that it represents two fused chromosome doublets, each with its own centromere. For more information about telomeres, go to Section 5: Telomeres & The End Replication Problem.

     Diagram of Chromosome Doublet Showing Centromere 

  11. Some biologists say that evolution is a scientific theory and a fact. According to T. Ryan Gregory of the Department of Integrative Biology, University of Guelph, Ontario, Canada (2007), the notion that species may change through time and that living organisms are related to one another through common descent is a fact. He also states that evolution is a well-established scientific theory. "That evolution is a theory in the proper scientific sense means that there is both a fact of evolution to be explained and a well-supported mechanistic framework to account for it. To claim that evolution is "just a theory" is to reveal both a profound ignorance of modern biological knowledge and a deep misunderstanding of the basic nature of science."

  12. The eminent evolutionary biologist Ernst Mayr also considers evolution to be a fact. In his book What Evolution Is (2001), he gives the following explanation:

    Is Evolution A Fact?

      "Evolution is not merely an idea, a theory, or a concept, but is the name of a process in nature, the occurrence of which can be documented by mountains of evidence that nobody has been able to refute. Some of this evidence was summarized in Chapters 1-3. It is now actually misleading to refer to evolution as a theory, considering the massive evidence that has been discovered over the last 140 years documenting its existence. Evolution is no longer a theory, it is simply a fact."

  13. The Working Group on Teaching Evolution, National Academy of Sciences (1998) defines a scientific theory as a well-substantiated explanation of some aspect of the natural world than can incorporate facts, laws, inferences, and tested hypotheses. Like "theory," the word "fact" has a different meaning in science than it does in common usage. A scientific fact is an observation that has been confirmed over and over. However, observations are gathered by our senses, which can never be trusted entirely. Observations also can change with better technologies or with better ways of looking at data. Please refer to paragraph 6 which discusses the erroneous human chromosome number of 48 and the planet Pluto. "Ironically, facts in science often are more susceptible to change than theories--which is one reason why the word "fact" is not much used in science."

  14. Eugenie C. Scott of the National Center For Science Education defines "facts" of evolution in the following paragraph:

      "From the standpoint of philosophy of science, the "facts of evolution" are things like the anatomical structural homologies such as the tetrapod forelimb, or the biochemical homologies of cross species protein and DNA comparisons, or the biogeographical distributions of plants and animals. The "facts of evolution" are observations, confirmed over and over, such as the presence and/or absence of particular fossils in particular strata of the geologic column (one never finds mammals in the Devonian, for example). From these confirmed observations we develop an explanation, an inference, that what explains all of these facts is that species have had histories, and that descent with modification has taken place. Evolution is thus a theory, and one of the most powerful theories in science."

  15. Richard Dawkins presents his case for why evolution should be called a fact rather than a theory in his book The Greatest Show on Earth: The Evidence For Evolution (2009). He refers to two kinds of theories: Well established scientific theories and laymen theories or tentative hypotheses. In fact, Dawkins compares a scientific theory with the mathematician's theorem, and proposes that scientific theory be replaced with the word "theorum." Two words with the same pronunciation and with different meanings and slightly different spellings will require even more clarification by writers and lecturers. In my opinion, capitalizing the word Theory for scientific theory would serve the same purpose, or better yet, just say scientific theory.

  16. The following paragraph comes from Chapter 2 of Anarchy Evolution by Greg Graffin and Steve Olson (2010):

      "Scientists believe that they can come closer and closer to something that can be described as "the truth" through observation, experimentation, and verification. They may never know if they have achieved the absolute truth--to the extent that such a thing can be defined. But if a statement has been tested so many times that there are no longer any resaonable grounds to suspect that further testing will reveal a discrepancy, scientists no longer refer to that statement as a theory or hypothesis. They call it a fact."

  17. The following definition of a fact comes from the National Academy of Sciences "Definitions of Evolutionary Terms" (accessed January 2011):

      "In science, a "fact" typically refers to an observation, measurement, or other form of evidence than can be expected to occur the same way under similar circumstances. However, scientists also use the term "fact" to refer to a scientific explanation that has been tested and confirmed so many times that there is no longer a compelling reason to keep testing it or looking for additional examples."

    Conclusion: Is Evolution Is A Theory Or A Fact?

  18. All of these discussions of whether evolution is a theory or a fact depend on how the terms "theory" and "fact" are defined. The "fact" that living organisms change or "evolve" with time is undeniable. In this sense evolution is certainly a fact. The complex mechanisms of evolution are best explained as a well-established scientific theory based on numerous facts. The position of Wayne's Word on teaching evolution is summarized by the Steering Committee on Science and Creationism, National Academy of Sciences (1999):

      "The contention that evolution should be taught as a "theory, not as a fact" confuses the common use of these words with the scientific use. In science, theories do not turn into facts through the accumulation of evidence. Rather, theories are the end points of science. They are understandings that develop from extensive observation, experimentation, and creative reflection. They incorporate a large body of scientific facts, laws, tested hypotheses, and logical inferences. In a sense, evolution is one of the strongest and most useful scientific theories we have."

  19. The Merriam-Webster Unabridged Third International Dictionary of the English Lanuage (1981) gives several definitions for the noun "fact:" (1) Something that has actual (tangible) existence. (2) An assertion, or statement containing something having objective reality. (3) Something proved by the evidence to be or alleged to be of actual occurrence. (4) A verified statement or proposition. (5) Something that makes a statement or a proposition true or false. (6) The reality of events or things, the occurrence or existence of which is to be determined by the evidence. The evolution of life on earth is certainly proven by factual evidence to be true; therefore, evolution can be called a fact under the Merriam-Webster definition.


    3. Evidence For Genetic Variability In Populations

  20. In order to have changes in populations of organisms it is necessary to have a source for the genetic variability. There are at least five sources of genetic variability in populations: (1) DNA mutations or changes in existing genes and the formation of new genes. (2) Reshuffling of chromosomes and genes during meiosis and sexual reproduction, including crossing over and transposons. (3) Natural selection for favorable traits, and selection against undesirable genes. (4) Interbreeding between genetically different populations, including emigration and immigration. (5) Genetic drift in relatively small, isolated populations.

    Details Of Mitosis & Meiosis
    An Introduction To Transposons
     Population Genetics & Genetic Drift 


    Genetic Variability & Neutral Theory Of Molecular Evolution

  21. The neutral theory of molecular evolution was proposed by the famous Japanese geneticist Motoo Kimura in the late 1960s and early 1970s. It basically states that the vast majority of evolutionary variations occur at the molecular level and are caused by random genetic drift of selectively neutral mutations not affecting fitness (Kimura, 1991). In other words, most of the genetic variation in populations is the result of DNA mutations and genetic drift and not selection. The theory suggests that if a population carries several different versions of genes, each of these versions is equally good at perforning its job and variation is neutral: Whether you carry gene version A or gene version B does not affect your fitness. When we see several versions of genes in a population, it is likely that their frequencies are simply drifting around. There are many examples of different versions of genes (alleles) in a population. For example, in the A-B-O blood types and Rh factor in humans there are several forms of genes that occur on homologous chromosomes. Some advocates of the neutral theory use human blood types as examples of the neutral theory; however, this theory is easily misinterpreted. These blood traits occur in chimpanzees and are very old. How can we be sure that they didn't convey some selective advantage in ancestral populations.

    Left: Multiple allele inheritance. The diagram shows one pair of homologous chromosomes, each with a single locus. Only one allele can occur at each locus, but there are 4 possible alleles per locus. Since the A1, A2, B and O alleles are located on one pair of loci on homologous chromosome pair #9, the following 10 genotypes are possible: A1A1, A1A2, A2A2, A1O, A2O, BB, BO, A1B, A2B and OO.

    Right: Polygenic Inheritance. The Rh factor is an interesting example of polygenic inheritance. Unlike the A-B-O blood types where all the alleles occur on one pair of loci on chromosome pair #9, the Rh factor involves three different pairs of alleles located on three different loci on chromosome pair #1. In the following diagram, 3 pairs of Rh alleles (C & c, D & d, E & e) occur at 3 different loci on homologous chromosome pair #1. Possible genotypes will have one C or c, one D or d, and one E or e from each chromosome. For example: CDE/cde; CdE/cDe; cde/cde; CDe/CdE; etc.

  22. In order to determine how many different genotypes are possible, you must first determine how many different gametes are possible for each parent, then match all the gametes in a genetic checkerboard. Although the three pairs of genes are linked to one homologous pair of chromosomes, there are a total of eight different possible gametes for each parent: CDE, CDe, CdE, Cde, cDE, cDe, cdE, and cde. This number of gametes is based on all the total possible ways these genes can be inherited on each chromosome of homologous pair #1. Since all three genes are closely linked together on the same chromosome, each gamete must contain one C (C or c), one D (D or d) and one E (E or e). The possible different genotypes are shown in the following table:

    Gametes
     CDE 
     CDe 
     CdE 
     Cde 
     cDE 
     cDe 
     cdE 
     cde 
    CDE
    CDE/
    CDE
    CDE/
    CDe
    CDE/
    CdE
    CDE/
    Cde
    CDE/
    cDE
    CDE/
    cDe
    CDE/
    cdE
    CDE/
    cde
    CDe
    CDe/
    CDE
    CDe/
    CDe
    CDe/
    CdE
    CDe/
    Cde
    CDe/
    cDE
    CDe/
    cDe
    CDe/
    cdE
    CDe/
    cde
    CdE
    CdE/
    CDE
    CdE/
    CDe
    CdE/
    CdE
    CdE/
    Cde
    CdE/
    cDE
    CdE/
    cDe
    CdE/
    cdE
    CdE/
    cde
    Cde
    Cde/
    CDE
    Cde/
    CDe
    Cde/
    CdE
    Cde/
    Cde
    Cde/
    cDE
    Cde/
    cDe
    Cde/
    cdE
    Cde/
    cde
    cDE
    cDE/
    CDE
    cDE/
    CDe
    cDE/
    CdE
    cDE/
    Cde
    cDE/
    cDE
    cDE/
    cDe
    cDE/
    cdE
    cDE/
    cde
    cDe
    cDe/
    CDE
    cDe/
    CDe
    cDe/
    CdE
    cDe/
    Cde
    cDe/
    cDE
    cDe/
    cDe
    cDe/
    cdE
    cDe/
    cde
    cdE
    cdE/
    CDE
    cdE/
    CDe
    cdE/
    CdE
    cdE/
    Cde
    cdE/
    cDE
    cdE/
    cDe
    cdE/
    cdE
    cdE/
    cde
    cde
    cde/
    CDE
    cde/
    CDe
    cde/
    CdE
    cde/
    Cde
    cde/
    cDE
    cde/
    cDe
    cde/
    cdE
    cde/
    cde

  23. You can also plug into this neat little formula for calculating the number of different genotypes based on the number of alleles per locus and the number of loci per chromosome. The formula was actually devised by several of my general biology students. It may occur somewhere in a textbook, but the students came up with it independently.


  24. There is ample evidence from field observations and DNA studies in laboratories to show that genetic variation occurs within populations of plants and animals. These are undeniable facts. The degree of variability is reflected in different levels of organization (taxonomic hierarchies), such as families, genera and species. DNA variations can be induced in the laboratory using mutagenic agents, such as strong chemical oxidizing agents and high energy radiation. Genetic variation can be readily observed in pathogenic bacteria that defy medical science by rapidly changing into new forms that are resistant to the latest antibiotics. HIV disguises itself from our highly evolved immune system and even acquires resistance to antiviral drugs, such as AZT. New strains of influenza viruses develop each year In fact, our war on pathogenic microbes has accelerated the process of microevolution in these organisms. Genetic variability is the raw material for this evolution. A thorough understanding of the genetics and evolution of pathogenic microorganisms may be crucial to the survival of the human race.

  25. DNA sequences coding for essential components of cellular metabolism, such as ribosomal subunits, are highly conserved, varying little between major groups of organisms. Highly conserved genes are very stable because changes in their DNA (mutations) are usually detrimental. Genes that are not highly conserved are subject to mutations and are important factors in natural selection and the evolution of new species. Some isolated species populations have unique traits correlated with geographic distribution. These populations are called subspecies, and their unique genetic changes have occurred through long periods of isolation. Varieties are similar to subspecies, but are not necessarily geographically isolated. Sometimes variation within a species complex makes identification very difficult. This is particularly true when the variable traits are apparently not under selection pressure and cannot be correlated with geographic distribution. One case in point is the California species known as BTK (Brodiaea terrestris ssp. kernensis), native to grasslands from Kern and Santa Barbara counties to the Mexican border. Most Brodiaea species have three sterile stamens called staminodes. Variants of BTK have staminodes that are hooded (curved inwardly at apex), staminodes that are flattened and strap-shaped or inrolled along upper margins, and narrow staminodes that are tapered toward the apex. In addition, the staminodes may be erect, leaning slightly outward or leaning inward. Statistical data from Principal Components Analysis (PCA) thus far indicates that BTK is one variable species complex; however, ongoing cladistical studies using chloroplast DNA may prove that some of these variants warrant segregation into species and subspecies or varieties.

    Staminode variation in BTK (Brodiaea terrestris ssp. kernensis): A. Otay Mtn (San Diego County), B. San Marcos (San Diego County), C. Sierra Nevada (Kern County), D. Gaviota Pass (Santa Barbara County), E. Santa Rosa Plateau (Riverside County).

  26. The primary explanation for the astonishing variety of life on earth is the amazing genetic molecule called DNA (deoxyribonucleic acid). DNA has been metaphorically described as a long, twisted ladder with literally millions of rungs composed of the base pairs: adenine (A) with thymine (T) and guanine (G) with cytosine(C). Each rung has 4 possible arrangements: A-T, T-A, C-G, and G-C. A DNA molecule with five billion base pairs has 45,000,000,000 or 103,000,000,000 different possible base sequences. This astronomical number has three billion digits and would fill about one million pages on a computer printout (12 cpi). This incredible number helps to explain the enormous diversity of life forms, from viruses and bacteria to complex plants and people, all genetically programmed by DNA. Flowering plants alone range from tiny wolffias less than one millimeter long to huge eucalyptus trees over 100 meters tall. The potential variability and mutability of DNA make it a perfect mechanism for evolution.

  27. DNA bases are to proteins as letters are to words. Different rearrangements and sequences result in numerous different proteins and words. Even a mutation in the DNA involving only one misplaced base (point mutation) may have a significant effect on the organism, particularly if this gene results in a crucial protein, such as a vital enzyme. A good analogy of a point mutation is a missplaced letter in a word. Like a point mutation in DNA, a one-letter substitution in a word can sometimes completely change the meaning of the sentence. This is especially true when speaking or writing in another language. In a store in Costa Rica I discovered that I had no Costa Rican currency called colones, only U.S. dollars. In my meager attempt to communicate with the clerk in Spanish, I told her that I had no "cojones," inadvertently substituting a "j" for an "l." When she replied: "I am sorry for you," I knew that my sentence was corrupted. In a vulgar translation, I essentially told the woman that I had no testicles! In this case, a one letter substitution (mutation) completely changed the meaning of the sentence.

    Table of DNA Base Triplets That Code For Specific Amino Acids

    Amino Acid
    DNA Base Triplets
    M-RNA Codons
    T-RNA Anticodons
    alanine
     CGA, CGG, CGT, CGC 
     GCU, GCC, GCA, GCG 
     CGA, CGG, CGU, CGC 
    arginine
    GCA, GCG, GCT, GCC
    TCT, TCC
    CGU, CGC, CGA, CGG
    AGA, AGG
    GCA, GCG, GCU, GCC
    UCU, UCC
    asparagine
    TTA, TTG
    AAU, AAC
    UUA, UUG
    aspartate
    CTA, CTG
    GAU, GAC
    CUA, CUG
    cysteine
    ACA, ACG
    UGU, UGC
    ACA, ACG
    glutamate
    CTT, CTC
    GAA, GAG
    CUU, CUC
    glutamine
    GTT, GTC
    CAA, CAG
    GUU, GUC
    glycine
    CCA, CCG, CCT, CCC
    GGU, GGC, GGA, GGG
    CCA, CCG, CCU, CCC
    histidine
    GTA, GTG
    CAU, CAC
    GUA, GUG
    isoleucine
    TAA, TAG, TAT
    AUU, AUC, AUA
    UAA, UAG, UAU
    leucine
    AAT, AAC, GAA, GAG
    GAT, GAC
    UUA, UUG, CUU, CUC
    CUA, CUG
    AAU, AAC, GAA, GAG
    GAU, GAC
    lysine
    TTT, TTC
    AAA, AAG
    UUU, UUC
    methionine
    TAC
    AUG
    UAC
    phenylalanine
    AAA, AAG
    UUU, UUC
    AAA, AAG
    proline
    GGA, GGG, GGT, GGC
    CCU, CCC, CCA, CCG
    GGA, GGG, GGU, GGC
    serine
    AGA, AGG, AGT, AGC
    TCA, TCG
    UCU, UCC, UCA, UCG
    AGU, AGC
    AGA, AGG, AGU, AGC
    UCA, UCG
    stop
    ATG, ATT, ACT
    UAA, UAG, UGA
    AUG, AUU, ACU
    threonine
    TGA, TGG, TGT, TGC
    ACU, ACC, ACA, ACG
    UGA, UGG, UGU, UGC
    tryptophan
    ACC
    UGG
    ACC
    tyrosine
    ATA, ATG
    UAU, UAC
    AUA, AUG
    valine
    CAA, CAG, CAT, CAC
    GUU, GUC, GUA, GUG
    CAA, CAG, CAU, CAC

    A Computer Screen Filled With DNA Code
    An Introduction To DNA Structure & Function
    Introduction To Polymerase Chain Reaction (PCR)
     Remarkable Diversity Of Flowering Plants On Earth 


    4. Origin Of Asexual Species: Populations With No Males

  28. The adaptive advantage of genetic variability through meosis and sexual reproduction has been well demonstrated, but what about the evolution of species without meiosis or sex? One of these remarkable cases is Fuller's rose weevil (Naupactus cervinus), a small flightless, broad-nosed weevil introduced into California from South America in the late 1800s. This beetle feeds on many cultivated plants and is especially troublesome in citrus groves where the adults eat new growth on young trees. The larvae feed on roots and make furrows in the bark. Eggs are laid on citrus fruits under the green calyx, and are transmitted during the shipment of infected fruits. Males have never been found in this species, so the females must produce viable eggs without fertilization, a phenomenon known as parthenogenesis. Each generation is composed of only females (thelytokous) that come from the same mother. According to Benjamin Normark (1996), parthenogenetic weevils are apomictic; meiosis does not occur and all female offspring are genetically identical to their mothers, except for mutations. Traditionally, hybridization and polyploidy were the main explanations for the origin of asexuality in weevils; however, Marcela Rodriguero, et al. (2010) suggests another possible explanation: the parthenogenesis inductor bacterium Wolbachia pipientis. The endosymbiont bacterial genome can produce drastic consequences on the evolution of its host species, such as extinction or sex role reversal. Assuming this species is haploid with one set of chromosomes, it certainly would not have the genetic variability and selection advantage of diploid populations with sexual repruduction. Nontheless, Fuller's rose weevil is a very successful insect. All mature adults can readily lay eggs, resulting in a serious agricultural pest in California.

  29. In a PBS TV broadcast about honey bees, the narrator referred to drone bees as "clones" of each other. Since clones are usually defined as genetically identical individuals (usually derived asexually), Wayne's Word strongly disagrees with the accuracy of this statement. Although the haploid drone comes from an unfertilized egg with only one set of maternal chromosomes, they are certainly not all genetically identical. The diploid queen bee undergoes normal meiosis (oögenesis) producing haploid eggs. During this meiotic process her 16 pairs of homologous chromosomes become altered by crossing over and reshuffled through random assortment, resulting in haploid eggs that are not chromosomally identical. In fact, with 16 pairs of homologous chromosomes, there are 216 or 65,536 different chromosomal combinations possible. Haploid drone bees produce haploid sperm in their testes through a mitotic spermatogenesis without a meiotic reduction division.

  30. Drone honey bee larvae develop within larger cells of the hive in order to accommodate the larger adult male. Worker bees develop in smaller cells from fertilized eggs and are essentially sterile females. The size of the cells is determined by workers who construct and mold the hexagonal wax cells with their mandibles; however, honeycomb cell size in sex determination is contradicted by K. Sasaki and Y. Obara (Zoological Science Volume 16, 1999) who reported fertilized eggs laid by queens in open areas outside honeycomb cells. Certain diploid worker larvae develop into fertile queens in much larger cells only if they are fed a special hormonal-nutrient mixture known as "royal jelly." The additional random combination of gametes during fertilization insures that worker bees are more genetically diverse than drones. With 216 or 65,536 different chromosomal combinations in the gametes, there are (216)2 or 4,294,967,296 different ways for the egg and sperm to combine. Since drone bees possess only maternal genes, a sister worker bee cannot share any paternal genes with her brother. Worker bees can inherit paternal genes from one set of drone chromosomes and maternal genes from two sets of queen chromosomes. Since the available gene pool is much greater for worker bees compared with drones, their genetic variability is greater. Therefore, the female workers contribute more to the Darwinian fitness of the species through natural selection. Although Darwin did not know about the genetics of honey bees, he was fascinated by their honeycomb cell-making instinct and devoted a dozen pages to the subject in Chapter 7 of The Origin of Species.

    Worker female honey bees (Apis mellifera) on their wax honeycomb. The honeycomb is composed of two layers of hexagonal cells. One layer of cells can be accessed from the front side, and another layer can be accessed from the back. This ingenious construction of the two layers of cells provides for the maximum utilization of space. The cells are used to store honey and larvae. Larger cells are constructed by the worker bees to accommodate the male drones which develop from unfertilized eggs. Extra large cells are used for larvae of fertilized eggs which are fed "royal jelly." These special females develop into sexually mature queens.

     The Sad Saga of the Drone Honey Bee 

  31. Entomologist Robert Page and his research team at the University of California, Davis have discovered the sex-determining "gender gene" (csd gene) in honeybees. Haploid drones have only one set of this gene per cell, while females have two sets. There are at least a dozen different forms of this gene (e.g. cds1, cds2, cds3, etc). Queen bees mate with many males, perhaps to insure that they get a good mix of different forms of the csd genes. If a queen mates with a male carrying her identical version of the csd gene, half of her fertilized eggs will develop into phenotypic sterile males, even though they are genetically diploid females with two sets of the same csd gene. These larvae are destroyed by worker bees. Apparently, two sets of identical csd genes will not function together.

    Queen (cds1/cds2)      X      Drone (cds1)
         50% cds1/cds2     
         
    50% cds1/cds1
         (destroyed by workers)     

    Fire ants that are currently invading the southern United States also have a similar sex-determining (csd) gene. They suffer from high levels of sterility, probably because they brought only a few versions of csd genes with them from South America. For beekeepers, inbreeding honeybees is a method of selecting docile insects that produce copious honey and reproduce rapidly; however, inbreeding also results in a high percentage of sterile males that are destroyed by workers. Pinpointing the precise "gender gene" in the sperm of males will enable beekeepers to produce disease-resistant, female honeybees containing different combinations of csd genes.

  32. In addition to male bees and wasps (order Hymenoptera) and short-nosed weevils (tribe Naupactini), there are other examples of parthenogenetic animals with no males. The virgin whiptail lizard (Cnemidophorus neomexicanus) of the western United States has only females in its population. One female mounts and clasps another female, presumably to induce ovulation. Because the genetic information has already been recombined in meiosis, the offspring are not identical clones of each other. Many species in the large insect order Homoptera (aphids & scale insects) also exhibit parthenogenesis with only females in their populations.

     Mitosis Compared With Meiosis 


    5. Gene Duplication: The Formation of New Genes

  33. In the previous section, mutations were listed as a source of genetic variability by the formation of new genes. Gene duplication plays such an important role in evolution that I have included a separate section about it. Gene duplication may involve single genes, chromosomes or the entire genome. It may be caused by translocations on the same chromosome, or by an error in the pairing of homologous chromosomes during meiosis where sister chromatids are out of alignment. Unequal crossing over can result is cells receiving extra genes and cells with deleted genes. Gene duplication in the laboratory is accomplished by the polymerase chain reaction (PCR). Using the PCR technique a single gene can be amplified or cloned into millions of duplicate copies. Plants are the most prolific gene duplicaters because they commonly form polyploids with multiple sets of the original base number of chromosomes. Most of our fruits and vegetables are polyploids, not to mention numerous wildflower species throughout the state of California.

    Simplified explanation for chromosome duplication during mitosis of a typical plant cell. In normal mitosis, the chromosome doublets separate during anaphase so that each of the daughter cells (far right) receives the exact same chromosome number as the original mother cell, i.e. four single chromosomes: two red and two blue. In this case, the anaphase cell divided into two daughter cells after the chromosome doublets had already separated into single chromosomes (i.e. chromatids separated). In other words, the spindle dissolved, leaving the cell with eight single chromosomes. These became doublets and the cell divided into two daughter cells each containing eight single chromosomes: four red and four blue. This phenomenon can be induced by the alkaloid colchicine.

     Polyploidy & Hybridization in California 
    The Major Details Of Mitosis & Meiosis

  34. According to Soltis, et al. (2003), old genomes that are polyploid with respect to the base number and amount of genetic material, may function as diploids with respect to the level of gene expression and chromosomal characteristics. These "old polyploids" may have become "diploidized" by the loss, mutation or suppression of duplicate genes. Other causes for diploidization may include genomic rearrangements and transposons. This can drastically change the chromosome properties of a species. For example, an odd polyploid with a base number of six might have a sporophyte number of 5n = 30. This pentaploid would tend to be sterile because of an odd chromosome set at synapsis of prophase I. However, if this plant behaves as a diploid with 2n = 30, it would be fertile with two sets of 15 chromosomes during meiosis. It would simply have a diploid (sporophyte) number of 2n = 30 and a haploid (gametophyte) number of n = 15. Diploidization has apparently occurred in the California genus Brodiaea. In fact, populations of B. terrestris ssp. kernensis in Kern County have a diploid chromosome number of 48, higher than a human somatic cell.

     Index Of Brodiaea Pages On Wayne's Word 
    Images Of Brodiaea Species In California

  35. Athough polyploid plants often have more chromosomes than people, the morphological complexity of an organism is certainly not reflected by the number of genes or DNA base pairs. For example, according to Gerald Tuskan of Oak Ridge National Laboratory, Tennessee (2006), the black cottonwood (Populus trichocarpa) genome has now been determined. His team identified more than 45,000 putative protein-coding genes. The Human Genome Project is a worldwide endeavor to map the DNA base sequence of every gene in the human genome. The total number of functional genes is considerably less than expected, about 30,000 genes per cell compared with previous estimates of 100,000 genes per cell. It has been estimated that a human somatic cell contains about 5 billion base pairs. If the average gene contains 1500 bases, then 30,000 functional genes is only about one percent of the total DNA per cell. It seems that some of this extra DNA came from gene duplication.

  36. The two genes that exist after gene duplication are called paralogs and usually code for proteins with a different function and/or structure. The second copy of the gene may be under less selective pressure because mutations of it have no deleterious effects on the host organism. Therefore, it mutates faster than a functional single-copy gene over generations of organisms. It should be noted here that gene duplication may not be passed on if it occurs in somatic cells. In addition, the duplication of oncogenes are known to be a common cause of certain types of cancer. The overall advantage of gene duplication is greatly increased genetic variability, the raw material for evolution. One of the truly remarkable examples of gene duplication is in the antibody mediated immune system of animals. How can we produce a seemingly endless array of germ-fighting antibody proteins in response to an infection?

    Immune (IgG) antibody model composed of four polypeptides: Two heavy (H) chains (longer green), and two light (L) chains (shorter blue). The two combining sites where the antibody "arms" attach to antigens are shown in red. Using this model, a separate gene for every antibody protein is not necessary. 1,000 genes could produce 1,000 different L chains and 1,000 genes could produce 1,000 different H chains. With 2,000 genes 1,0002 or 1,000,000 different antibodies could be produced, simply by using different combinations of H chains and L chains. This may explain how organisms can produce antibodies against different antigens, even synthetic antigen proteins that animals have never been exposed to. Using this model, animals would not need separate genes for every antigen that they will ever encounter, they simply manufacture millions of different possible antibodies from a given number of genes for L chains and H chains. The reservoir of L and H chains comes from gene duplication.

  37. Another example of gene duplication is the evolution of color vision (trichromacy) in higher primates. [See G.H. Jacobs and J. Nathans Scientific American 300 (4): 56-63, April 2009.] This remarkable property of human vision is possible because the retina (the layer of nerve cells in the eye that captures light and transmits visual information to the brain) uses only three types of light-absorbing pigments for color vision. Each individual cone cell in the retina contains genes for all three color pigments, but randomly selects only one of the three to activate and shuts down the other two. The M and L pigment genes reside on the X chromosome, and a third S pigment gene is located on chromosome #7. Each of the three pigments absorbs light from a particular region of the spectrum and collectively produce a wide range of color vision. The pigments absorb light of different wavelengths that we perceive as yellow, green and blue. This phenomenon is similar to the the mixing of red, green and blue pixels to generate a full spectrum of color in computer monitors. The following table shows 216 color combinations produced from three colors using a six character hexadecimal HTML code:

    Different Colors Produced By 6 Character HTML Hexadecimal Code
    216 Color Combinations From 000000 (black) to ffffff (white)

    000000
    000033
    000066
    000099
    0000cc
    0000ff
    006600
    006633
    006666
    006699
    0066cc
    0066ff
    00cc00
    00cc33
    00cc66
    00cc99
    00cccc
    00ccff
    003300
    003333
    003366
    003399
    0033cc
    0033ff
    009900
    009933
    009966
    009999
    0099cc
    0099ff
    00ff00
    00ff33
    00ff66
    00ff99
    00ffcc
    00ffff
    330000
    330033
    330066
    330099
    3300cc
    3300ff
    336600
    336633
    336666
    336699
    3366cc
    3366ff
    33cc00
    33cc33
    33cc66
    33cc99
    33cccc
    33ccff
    333300
    333333
    333366
    333399
    3333cc
    3333ff
    339900
    339933
    339966
    339999
    3399cc
    3399ff
    33ff00
    33ff33
    33ff66
    33ff99
    33ffcc
    33ffff
    660000
    660033
    660066
    660099
    6600cc
    6600ff
    666600
    666633
    666666
    666699
    6666cc
    6666ff
    66cc00
    66cc33
    66cc66
    66cc99
    66cccc
    66ccff
    663300
    663333
    663366
    663399
    6633cc
    6633ff
    669900
    669933
    669966
    669999
    6699cc
    6699ff
    66ff00
    66ff33
    66ff66
    66ff99
    66ffcc
    66ffff
    990000
    990033
    990066
    990099
    9900cc
    9900ff
    996600
    996633
    996666
    996699
    9966cc
    9966ff
    99cc00
    99cc33
    99cc66
    99cc99
    99cccc
    99ccff
    993300
    993333
    993366
    993399
    9933cc
    9933ff
    999900
    999933
    999966
    999999
    9999cc
    9999ff
    99ff00
    99ff33
    99ff66
    99ff99
    99ffcc
    99ffff
    cc0000
    cc0033
    cc0066
    cc0099
    cc00cc
    cc00ff
    cc6600
    cc6633
    cc6666
    cc6699
    cc66cc
    cc66ff
    cccc00
    cccc33
    cccc66
    cccc99
    cccccc
    ccccff
    cc3300
    cc3333
    cc3366
    cc3399
    cc33cc
    cc33ff
    cc9900
    cc9933
    cc9966
    cc9999
    cc99cc
    cc99ff
    ccff00
    ccff33
    ccff66
    ccff99
    ccffcc
    ccffff
    ff0000
    ff0033
    ff0066
    ff0099
    ff00cc
    ff00ff
    ff6600
    ff6633
    ff6666
    ff6699
    ff66cc
    ff66ff
    ffcc00
    ffcc33
    ffcc66
    ffcc99
    ffcccc
    ffccff
    ff3300
    ff3333
    ff3366
    ff3399
    ff33cc
    ff33ff
    ff9900
    ff9933
    ff9966
    ff9999
    ff99cc
    ff99ff
    ffff00
    ffff33
    ffff66
    ffff99
    ffffcc
    ffffff

  38. Most nonprimate mammals exhibit dichromacy, with color vision based on just two kinds of visual pigments. These animals do not have full color vision. Although the mechanism of gene inactivation is slightly different in Old and New World primates, the evolution of trichromacy enabled these mammals to see a technicolor world of flowers, fruits and insects. This is somewhat analogous to the evolution of high resolution color monitors from the drab monochrome green and amber progenitors. One obvious advantage of trichromacy is being able to clearly distinguish the subtle shades of ripening fruit from surrounding vegetation.

  39. Color blindness or the inability to differentiate between certain color variations is more common in men because they have only one X chromosome. If defective M and L pigment genes reside on their single X chromosome, men will exhibit this trait. Women have two X chromosomes and therefore can be homozygous or heterozygous for the color blind trait. The phenomenon of X inactivation complicates the expression of color blindness in heterozygous females since only one X is functional and the other remains inactive as a Barr body. The inactivation of X chromosomes appears to be a random event.

     The Inheritance Of Color Blindness In Humans 


    6. Telomeres: A Major Molecular Fix To A Chromosome Replication Problem

  40. The structure and function of DNA are certainly two of the most significant discoveries that have revolutionized the science of biology. Even though DNA appears to be a perfect storage molecule for genetic information, it has a serious replication problem. Chromosomes of eukaryotic cells are composed of linear DNA. In order for cell division to take place, the DNA molecule must replicate. In other words, the single chromosome must become a doubled chromosome composed of two chromatids. The problem is that each time DNA replicates the new molecules get slightly shorter. After a number of consecutive divisions, this degradation could result is serious gene loss at the ends of the chromosomes. Both Alexey Olovnikov and James Watson independently described this phenomenon called "end replication problem" in the early 1970s. In fact, Olovnikov's "A Theory of Marginotomy" predicted that the loss of terminal sequences resulting from end replication problem would lead to senescence (Olovnikov, 1973). [James Watson and Francis Crick discovered the structure of DNA in 1953 and received the Nobel Prize in Medicine in 1962.]

  41. To cope with the devastating end problem replication problem, eukaryotic cells have evolved protective "caps" on the ends of chromosomes called telomeres. For their discovery of how chromosomes are protected by telomeres and the enzyme telomerase, Elizabeth Blackburn, Jack Szostak and Carol Greider were awarded the Nobel Prize in Medicine in 2009. With their ingenious genetic research and meticulous biochemical studies, they not only solved a fundamental problem in biology but also opened a new field of research and initiated the development of potential therapies against the aging process and cancer. It should be noted here that more than 60 years earlier, Barbara McClintock was studying telomeres in corn. In the early 1940s she turned her attention to the study of transposable elements (transposons) in corn, another remarkable genetic phenomenon with important medical implications in people. For her lifelong research on transposons, she received the Nobel Prize in Medicine in 1983.

    Cell Division (Mitosis) In Eukaryotic Cells
    Major Chemical Compounds Of Life (Part 1)
    DNA and Polymerase Chain Reaction (PCR)
     Transposons: Transposable "Jumping" Genes 

  42. Telomeres are repetitive strands of DNA (sequences of repetitive bases) at the terminal ends of linear chromosomes. They play an essential role in maintaining the integrity of the chromosome by protecting it from degradation and from end-to-end fusion with other chromosomes. Telomeres are essentially protective "end caps" of non-coding DNA at the extreme ends of chromosomes. Telomeres have been metaphorically compared with the tips of shoelaces that keep the laces from unraveling. Each time a cell divides, the telomeres lose a small amount of DNA. Eventually, when all of the telomere DNA is gone, the cell can no longer divide and dies. End replication problem is not an issue in prokaryotic cells because they have circular DNA molecules without ends.

  43. The number of times a population of normal cells can divide is called the Hayflick limit, named after its discoverer Leonard Hayflick. In 1961, Hayflick demonstrated that normal human fetal cells in a culture divide between 40 and 60 times. It is now clear that cell division occurs until the telomeres reach a critical length. An estimated length for human telomeres ranges from 8,000 base pairs at birth to 3,000 as people age, and as low as 1,500 in elderly people. Starting with 8,000 base pairs, a loss of 100 to 200 with each division would completely erode away the telomeres in 40 to 80 divisions.

    Prerequisites For DNA Polymerase:

    1.  When DNA Unzips, DNA Polymerase Must Attach To 3' End of Mother Strand.
    2.  It Must Add Nucleotides (Synthesize Daughter Strand) In The 5' to 3' Direction.
    3.  An RNA Primer Must Attach First To Give DNA Polymerase A Place To Start.

  44. Chromosome duplication starts with the unzipping of the double stranded DNA into two strands (mother strand #1 & mother strand #2). These complementary mother strands serve as templates to build two DNA molecules. An RNA primer attaches to the 3' end of mother strand #1, thus giving DNA polymerase a place to start. The primer attaches just before the initial attachment of DNA polymerase. DNA polymerase moves in the 3' to 5' direction along mother strand #1, adding nucleotides to form a continuous complementary daughter strand of DNA the entire length of the mother strand #1 template. This complementary strand is called the "leading strand" and it is synthesized in the 5' to 3' direction. [5' and 3' refer to specific carbon atoms of deoxyribose sugar in DNA building blocks called nucleotides.] When 5' and 3' directions are mentioned, it is important to specify whether you are referring to the mother strand or the complementary daughter strand.

  45. As the original mother DNA unzips, DNA polymerase cannot attach to the top of mother strand #2 at the 5' position (top right in following diagram). Even if it could attach to the top of mother strand #2 at the 5' position, it could not move down the mother strand and synthesize a daughter strand in the 3' to 5' direction. Therefore, DNA polymerase attaches farther down on mother strand #2 and produces a series of DNA sections in the 5' to 3' direction. These sections are named "Okazaki fragments" after the Japanese scientist Reiji Okazaki who discovered them. The sections collectively form a daughter strand called the "lagging strand" to the top of mother strand #2. This is nicely explained by R. Ohki, T. Tsurimoto and F. Ishikawa (Molecular and Cellular Biology Vol. 21, 2001). Short RNA primers must attach ahead of each DNA section in order to form a starting point for DNA polymerase.

  46. There is a problem at the 3' end of mother strand #2. When the last RNA primer reaches this end, there is no more DNA template for it to keep ahead of DNA polymerase. The last primer attaches to the 3' end, but DNA polymerase cannot add the last section of the lagging strand, leaving a gap where the primer was attached. Therefore, the 5' end of each newly synthesized lagging strand is cut short. About 100 base pairs are shaved off with each round of replication, thus shortening the telomere. In the following diagram, mother strand #2 has a gap at the 5' end of the newly formed lagging strand.

    The following animated gifs show replication of DNA in six consecutive divisions without any shortening, compared with the end replication problem on lagging strand and the gradual shortening of DNA.

      See Animation Of DNA Replication  

  47. Telomeres can be restored by the enzyme telomerase. This enzyme lengthens telomeres in germ cells (cells that produce eggs and sperm), thus restoring telomeres to their maximum length in the zygote. It is also present in other cells that must continually divide, including bone marrow stem cells that produce large numbers of generations of red blood cells necessary to sustain life, the epithelium of skin, and cells lining the intestine. Telomerase is generally not active in normal somatic cells. This enzyme adds noncoding DNA sequence repeats TTAGGG in vertebrates to the 3' end of DNA strands in the telomere region of eukaryotic chromosomes. The presence of active telomerase in cancer cells may be useful in the diagnosis and treatment of some cancers with telomerase inhibitors.

  48. The following paragraph comes from Science and Technology (9 November 2007): Sharks have telomerase in all of their cells. Their telomeres don't shorten and sharks do not have a genetically programmed life span like humans. In fact, sharks keep growing throughout their life. The limit to their life span is the fact that they must keep moving in order to circulate air through their gills for the uptake of oxygen. Sharks are exceptionally genetically stable, having changed very little in hundreds of millions of years. In addition, sharks rarely get cancer.

  49. Telomeres and telomerase also occur in plant cells. Plant telomere biology is summarized by T.D. McKnight and D.E. Shippen in The Plant Cell Vol. 16: 794-803 (2004). In most flowering plants, telomeres consists of the DNA base repeats TTTAGGG. Like the somatic cells of animals, there is little or no active telomerase in vegetative tissue, although it is reactivated during flowering, probably to ensure that gametes and embryos inherit telomeres restored to their maximum length. Like cancer cells in in animals, telomerase is fully functional in cells of plant tissue cultures, as might be expected for cells with an unlimited capacity for proliferation. The monocot order Asparagales that contains about 27,000 species (roughly10 percent of all angiosperms) has 6-base repeats of TTAGGG, the same sequence found in mammalian telomeres. This order includes many familiar plant families, such as orchids, iris, amaryllis, agave, onion and asparagus. Since plants and mammals evolved into multicellular organisms along completely separate pathways, this appears to be yet another example of parallel evolution (homoplasy).

  50. Telomeres do not prevent the shortening of DNA, they just postpone the erosion process. The telomere shortening mechanism normally limits cells to a fixed number of divisions. Eventually, when all of the telomere is gone, the cell can no longer divide, thus terminating the cell cycle. Most cancer's are the result of "immortal" cells which have evaded programmed cellular death due to erosion of telomeres. Chromosomes of malignant cells usually do not lose their telomeres, thus resulting in uncontrolled cell division. Animal studies suggest that telomere length may be related to the aging process on the cellular level and the life span of animals. There are even studies suggesting that regular exercise and stress reduction may help to minimize telomere erosion. In fact, a study published in the May 3, 2005 issue of the American Heart Association journal Circulation found that weight gain and increased insulin resistance were correlated with greater telomere shortening over time.

    Diagram of Chromosome Doublet Showing Centromere
     The Structure Of Cell Membranes & Insulin Resistance 

  51. It is interesting to speculate on the origin of telomeres. If another version of DNA polymerase existed that attached to the 5' end of mother strand #2 and added nucleotides in the 3' to 5' direction, then theoretically a continuous strand could be synthesized to the end of the mother strand template without the end replication problem. This theoretical version has never been found and therefore telomeres are essential to prevent the gradual shortening of DNA and erosion of genes. Why is there only one form of DNA polymerase that synthesizes daughter strands in the 5' to 3' direction? This is like asking why living systems only have L-form (left handed) amino acids and D-form (right handed) sugars. Did the evolution of telomeres solve a replication problem inherent in the original DNA, or were telomeres present in the original DNA of the first eukaryotic cells?

    Evolutionary Significance of End Problem Replication & Telomeres

  52. When I first wrote this section about end replication problem, I concluded that it was a defect in DNA that literally shortened the life of a cell by limiting the number of divisions. Telomeres serve as mitotic time clocks that prolong life by a certain number of consecutive erosions. However, there is another side to this story where limiting the life span of organisms could actually be beneficial. In a rapidly changing environment, survival of a species depends on genetic variability through DNA mutations and the ability to pass these genes on to future generations. A species with exceedingly long generation times may not be able to compete because adaptive mutations can't keep up with environmental changes; however, longer generation spans could also slow population growth as long as fecundity (number of offspring per female) remains constant. To an individual, immortality may seem good; however, this may not be good for the species. This logic is mentioned in Star Trek 2: "The Wrath of Khan" when Spock said: "The good of the many outweighs the good of the few, or the one." Actually, this logic is mentioned two thousand years earlier in John 11:49-50. Of course, one caveat to the benefit of end replication loss is the shark, which apparently has active telomerase in all of its cells and telomeres lengths that don't decline significantly with age. Sharks (class Chondrichthyes) are a very successful group and they have been around for more than 200 million years. In fact, some species have age estimations of 100 years or more. Undoubtedly, environmental changes in the ocean have not been as rampant as on land.

     Principles Of Population Growth 


    7. Evolution & Irreducible Complexity

  53. Coagulation or the clotting of blood is a complex process which evolved from repetitive gene duplication. It involves platelets and the clotting protein fibrin plus a series of enzymatic reactions called the coagulation cascade. Disorders of coagulation can lead to an increased risk of bleeding (hemorrhage) and/or clotting (thrombosis). So crucial is this elaborate cascade, that one failed protein can disrupt the entire process. Intelligent design advocate Michael Behe (1996) has argued that coagulation is an example of irreducible complexity, where less complex models simply could not exist. In other words, each and every element of the complex cascade of enzymes and cofactors must be in place for blood clotting to work. According to Behe (Darwin's Black Box, 1996), an irreducibly complex system cannot be produced by Darwinian natural selection, and must have been "designed." However, Kenneth Miller ( Finding Darwin's God, 1999) discusses Russell Doolittle's pioneering work on protein evolution and the mechanism of blood coagulation. Miller describes a simpler blood clotting system in a lobster whose step-by-step evolution is relatively easy to account for. Behe also uses irreducible complexity in his description of the common mousetrap, an oversimplified argument that has been clearly refuted by other scientists. In fact, please refer to the following web pages by Keith Robison (1996) and John H. McDonald (2002).

     Irreducible Complexity or Irreproducible Irreducibility 
    Animations Showing A Reducibly Complex Mousetrap

  54. Another example of irreducible complexity that is often used by advocates of intelligent design is the remarkable bombardier beetle (Brachinus). How could such a complex and potentially lethal mechanism for repelling predators be produced by natural selection? This suborder of beetles known as Adephaga secrete a number of chemicals for a variety of purposes, only one of which is defense. Bombardier beetles inject an explosive mixture of hydroquinone, hydrogen peroxide plus several potent catalysts into a reaction chamber in the abdomen. Catalase breaks down the hydrogen peroxide into water and oxygen gas. Peroxidase oxidizes hydroquinone into benzoquinone. The mixture of chemicals and enzymes volatilizes instantly upon contact with the air, generating a puff of "smoke"" and an audible popping sound. This caustic flatulence is totally controlled by the beetle, otherwise it might accidentally blow up its rear end. The explosive discharge apparently discourages predators, either by chemical irritation, heat or repugnance. The temperature of the explosive mixture of gasses and fluids is over 100 degrees Celsius, the boiling point of water. This astonishing chemical defense mechanism is discussed by D.J. Aneshansley and T. Eisner (1969) in Science Vol. 165: 61-63.

    Bombardier beetles of the genus Brachinus, a member of the large ground beetle family (Carabidae). These small beetles are about 13 mm long (1/2 inch). They are fairly common in southern California, particularly near streams, lakes and marshy areas. The wing covers (elytra) are dark blue-brown with a contrasting reddish-orange head and prothorax.

  55. Other arthropods also produce some of the same chemicals found in bombardier beetles. Like bombardier beetles, these chemicals are used for defense or make the animal distasteful to predators; however, the mechanisms are not as sophisticated as bombardier beetles. Starting with these simpler mechanisms, a plausible step-by-step microevolutionary pathway culminating in bombardier beetles can be constructed. In fact, Mark Isaak (2003) discusses this in his on-line article entitled: "Bombardier Beetles and the Argument of Design."

     The Origin Of Eyes In Distantly Related Animals 


    8. Scientific Theory vs. Common Theory

  56. A scientific theory is a testable (verifiable & falsifiable) explanation about the cause or causes of a broad range of related phenomena. It remains open to tests, revision, and tentative acceptance or rejection. It should not be confused with a common layman theory or proposition that has not been scrutinized by the scientific method. In the scientific method, a hypothesis or tentative explanation is formulated to explain an observation or phenomenon. This is a good example of inductive reasoning where a general conclusion (hypothesis) is based on specific observations or data. Then an attempt is made to prove or disprove the hypothesis through detailed research and experimentation. Successful results by one scientist does not automatically turn a hypothesis into a theory. "One scientist cannot create a scientific theory; he or she can only create a hypothesis." Only after repeated tests by other scientists who arrive at similar conclusions does a hypothesis become a scientific theory. Evolution is not merely a common theory or "only a theory" as some people state in their commentaries. It is a scientific theory based on more than a century of research by thousands of dedicated scientists from throughout the world.

  57. Biological evolution has considerable empirical evidence, and it is testable and verifiable. It fits the definition of a true scientific theory. Under a strict definition, a scientific theory should not be called a "fact" even though it explains all known facts and has survived the test of time (more than a century in the case of evolution). There is always the possibility that a scientific theory will be updated or changed as new evidence is discovered. The sticker placed in biology textbooks in Atlanta is poorly worded. It implies that evolution is just another "common theory," a tentative statement that attempts to explain something without any factual proof. A common theory has a popular meaning, which is roughly equivalent to an "educated guess" or "hunch." The label should say "scientific theory" rather than theory. In addition, the dichotomous comparison of a scientific theory with the word "fact" is incorrect.

  58. As stated above, all interpretations of facts in science are provisional and subject to challenge. Physicists never refer to any theory as a "fact," and always leave open the possibility that any theory will be found to be incomplete or needing revision, even though it fits all known facts and has passed all tests so far. It is still Einstein's theory of relativity, even though it is probably as close to a fact as anyone can get in science. It has been tested every day in many ways and has survived. Some day we may find a more complete theory that explains and predicts relativity even better than Einstein's theory. The noun "theory" associated with time-tested explanations, such as evolution, relativity and plate tectonics, should be modified by the adjective "scientific" in order to distinguish it from a "common" or "layman" theory that is essentially a tentative explanation or untested hypothesis. In fact, it would be better to capitalize the word theory when it refers to a scientific theory. [For example, gram calories and dietary Calories are spelled the same, except that a dieter's Calorie is capitalized and actually refers to a kilocalorie!]

  59. It should be noted here that a hypothesis does not always become a scientific theory. Here is an example: A botanist discovers a wildflower population that appears different from all other known species of a particular genus. His hypothesis states that this is a new (undescribed) species unknown to science. To prove this hypothesis it is necessary to collect numerous detailed measurements of the floral and vegetative parts and to conduct an extensive search of the literature and herbaria. A type specimen (holotype) of the plant is deposited in an internationally recognized herbarium. Duplicated specimens (isotypes) are deposited in other herbaria. The hypothesis is confirmed by statistical analysis of the data, including PCA (principal components analysis). The results are published in a peer-reviewed botanical journal. Generally, this hypothesis is not elevated to the level of a scientific theory. It can be reviewed by another botanist who may accept or reject the species status, perhaps by performing additional tests, such as DNA sequencing. This was essentially the method used by this author in coauthoring a new species of Brodiaea in 2007 named Brodiaea santarosae; however, in our particular case, the hypothesis for a new species came after our preliminary statistical investigation.

    Brodiaea santarosae On The Santa Rosa Plateau
    Lecture Notes On The Santa Rosa Basalt Brodiaea
    Article Published In Madrono Vol. 54: 187-198 (2007)
     Images of Brodiaeas In Central & Southern California 


    9. Explanations For Moving Rocks Of Racetrack Playa: Theories or Hypotheses?

    The sliding (sailing) rocks on Devil's Racetrack move in different directions.

  60. The mysterious moving rocks of Racetrack Playa in Death Valley National Park have baffled scientists for decades. Although several plausible explanations have been proposed, no one has actually filmed this remarkable phenomenon in motion or observed it in real time. A few explanations are controversial and not agreed upon by all scientists, and a thorough verifiable and well substantiated proof appears to be lacking. Unfortunately, most references refer to these explanations as theories. As of January 2010 the explanations for this remarkable phenomenon appear to be scientific hypotheses and have not become a comprehensive scientific theory. One thing is certain: The rocks definitely change position with time, and this multidirectional movement has been verified by GPS measurements.
  61. Several hypotheses have been proposed to explain the sliding ("sailing") rocks across the lakebed. Most authorities agree with at least two conditions necessary for the movement of rocks. (1) Occasional heavy rains and runoff from nearby slopes producing a slick surface on the fine clays of the lakebed. (2) Gail force, multidirectional winds of at least 80-100 miles per hour, strong enough to push the rocks across the surface in different directions. (3) A third hypothesis builds upon the previous ones and appears to be necessary for larger rocks weighing up to 700 pounds. Freezing nighttime winter temperatures that produce a floating ice sheet on the muddy clay surface. As the lakebed dries, the clay mud shrinks and cracks into a mosaic of interlocking polygons. When the playa fills with water, the fine clay imbibes water and the polygonal cracks coalesce into a sticky surface. Another hypothesis describes colonies of cyanobacteria living in the surface clay that also imbibe water and become mucilaginous, possibly contributing to the slippery surface. Filamentous cyanobacteria secrete a mucilaginous sheath that helps to bind soil particles together in microbial communities known as cryptobiotic crust.

     Cryptobiotic Crust In Anza-Borrego Desert State Park 

  62. There are additional hypotheses to explain the movement of rocks, however, most of these can be discounted. Gravity can be ruled out since the north end of the lakebed is 1.5 inches (4 cm) higher than the southern end, and most of the rocks traveled slightly uphill. Pranksters during wet years is a possibility, except they left no footprints in the soft, muddy clay surface adjacent to the rocks. Another hypothesis involves aliens from another planet who visited this playa during exceptional wet years.

     More Images Of Racetrack Playa In Death Valley National Monument 


    10. The K-T Boundary & Demise Of The Dinosaurs

    About 70 million years ago, eastern Montana was a vast subtropical swampland with a lush forest that supported numerous dinosaurs, including Tyrannosaurus rex. Today this area is an arid badlands composed of sedimentary strata containing the fossilized remains of a diverse flora and fauna. The above painting is on the outside wall of the Makoshika Dinosaur Museum in downtown Glendive, Montana.

  63. The K-T (Cretaceous-Tertiary) boundary is a dark, narrow band of sediments and carbonized plant material (coal) that separates the Cretaceous and Tertiary periods about 65 million years ago. In Makoshika Stae Park the tan strata above the K-T band is called the Fort Union Formation. It is younger than 65 million years and does not contain dinosaur fossils. The term Paleocene ("early-recent") refers to a time period when dinosaurs were replaced by smaller mammals, long before modern mammalian orders emerged. Below the K-T band is the older brownish-gray Hell Creek Formation that is rich in dinosaur fossils, including Tyrannosaurus rex, Triceratops and the amazing duck-billed Hadrosaurus. It also contains the fossilized fruits of an extinct palm (Spinifructus antiquus), once thought to be an extinct fig.

     Ancient Ficus ceratops May Not Be A Fig! 

  64. The best explanation (scientific theory) for the mass extinction of non-avian dinosaurs is an enormous 10 km (6 mile) diameter asteroid that collided with the earth about 65 (65.5) million years ago causing a global dust cloud that blotted out the sun for many months. In 1980, a team of researchers consisting of Nobel prize-winning physicist Luis Alvarez, his son, geologist Walter Alvarez, and chemists Frank Asaro and Helen Michels discovered that sedimentary layers found all over the world at the K-T boundary contain a concentration of iridium many times greater than normal. Iridium is a rare earth element that is abundant in most asteroids and comets. It is the second densest element after osmium and the most corrosion-resistant metal. The Alvarez team suggested that an asteroid struck the earth at the time of the K-T boundary.

  65. This explanation for the rapid demise of non-avian dinosaurs is based on a lot of research and published data from many independent scientists from around the world. It is much more than a mere hypothesis. Estimates as high as 85 percent of all species disappeared from the face of the earth at this time. This catastrophic event forever changed the direction of the evolution of life on earth.

    Badlands of Makoshika State Park near Glendive, Montana.


    11. Scientific Theory & Scientific Law

  66. As I stated previously, the Working Group on Teaching Evolution, National Academy of Sciences (1998) defines a scientific theory as a well-substantiated explanation of some aspect of the natural world than can incorporate facts, laws, inferences, and tested hypotheses. They define a scientific law as a descriptive generalization about how some aspect of the natural world behaves under stated circumstances. Laws can be very useful in supporting hypotheses and theories, but like all elements of science they can be altered with new information and observations. Scientific theories and scientific laws are both derived from carefully formulated hypotheses that have been scrutinized and repeatedly tested by scientists. In general, they are both accepted to be true by the scientific community and they are both used to make predictions of events. The notion that scientific theories eventually become laws is incorrect. Scientific theories are generally more complex and dynamic than scientific laws; they have many components, and may be changed as the body of available experimental data and analysis develops. In addition, scientific theories explain a whole series of related phenomena. Examples of scientific theories include the chaos theory in mathematics, the theory of relativity in physics, and the theory of plate tectonics and continental drift in geology.

  67. Scientific laws are strictly empirical and explain a single action or set of actions. They can sometimes be expressed in terms of a single mathematical equation. Examples of scientific laws include the laws of thermodynamics, Newton's law of gravity, Hook's law of elasticity, Ohm's law, and the gas laws (Boyle's law and Charles' law). Scientific laws may be components of scientific theories. For example, Newton's law of gravity is contained within Einstein's theory of relativity. Mendel's laws of segregation and independent assortment refer to specific mechanisms of the inheritance of genes. They were once hypotheses used by Gregor Mendel in 1865 to explain the inheritance of specific traits in garden peas, such as round vs. wrinkled and yellow vs. green peas. His original hypothesis explained the observed 9:3:3:1 ratios obtained from his dihybrid crosses. Mendel's laws are essential components of the modern theory of evolution; however, there are exceptions to these laws. When Mendel completed his research on genetic crosses with garden peas, he assumed that the individual traits were assorted independently of each other. One of his hypotheses became known as the Law of Independent Assortment. Today we can explain this law because the traits Mendel studied just happened to occur on separate chromosomes. Since the garden pea has 7 pairs of chromosomes, it is obvious that all the hundreds of genes in peas cannot occur independently of each other, and must be located on 7 pairs of homologous chromosomes. Depending on the exact genes you are studying, chromosomal linkage may result in ratios of offspring that are far different from the 9:3:3:1 predicted by Mendel. Laws and theories are the foundations of scientific knowledge; together they explain our complex natural world. They can be modified or changed as more information is available.

     Dihybrid Cross In Corn Similar To Mendel's Crosses With Garden Peas 
    Smooth vs. Shrunken grains instead of Round vs. Wrinkled peas
    Purple vs. Yellow grains instead of Yellow vs. Green peas

  68. In 1908 English mathematician Godfrey Hardy and German physicist Wilheim Weinberg independently came up with an algebraic expression that describes how genotype frequencies in populations are related to allele frequencies. Known as the Hardy-Weinberg Law, it states that gene frequencies will remain constant generation after generation in large, randomly-mating populations. Although it is a law, it is only applicable under a strict set of conditions, including no mutations, no selection, no migrations between populations (immigration and emigration), and no genetic drift. In a 2-allele system, such as round and wrinkled peas, it is based on the square of a binomial (A + B). In a 3-allele system, such as the A-B-O blood types, it is based on the square of a trinomial (A + B + O). Although it is beyond the scope of this discussion, the Hardy-Weinberg Law is useful for studies in population genetics, particularly the determination of genotype frequencies in populations.

    Percentages Of Blood Genotypes In Hypothetical Population
    There Are 4 Phenotype Percentages Including: 32% Type A (Red),
    15% Type B (Green), 4% Type AB (Blue) and 49% Type O (Brown)

    Alleles
    0.2   A
    0.1   B
    0.7   O
    0.2   A
    AA    4%
    AB    2%
    AO    14%
    0.1   B
    AB    2%
    BB    1%
    BO    7%
    0.7   O
    AO    14%
    BO    7%
    OO    49%

    6 Genotypes In Above Table Appear In The Trinomial Expansion (A + B + O)2 =
    A2 (4%) + 2AB (4%) + B2 (1%) + 2AO (28%) +2BO (14%) + O2 (49%)

     See Population Genetics Page 


    12. Evidence For Evolution Based On Fossils & Cladistics

  69. A fascinating article about evidence for evolution was written by David Quammen in the November 2004 issue of National Geographic. Evidence for evolution comes from many disciplines, including paleontology, biogeography, anatomy, embryology, physiology, biochemistry and cladistics. Most of Darwin's arguments for evolution in his original Origin of Species (1859) were based almost exclusively on evidence from living organisms (Prothero, 2007). In modern cladistical analysis, computers create elaborate phylogenetic trees or cladograms from DNA sequences containing thousands of base pairs. The cladogram "trees" are organized from the most primitive organisms to the most advanced. The number of shared characteristics between any one species and another indicates how recently these two species have diverged from a shared lineage. Sometimes the cladograms fit the existing models based on fossil evidence and sometimes they do not. Whale paleontologist Peter D. Gingerich collected fossil specimens of early whales from remote areas of Egypt and Pakistan. His research traced the ancestry of whales back to a group of Eocene carnivorous mammals called mesonychids. Evidence from DNA comparisons suggests that whales descended from artiodactyls (even-toed, hooved mammals, such as antelopes, pigs and hippos). Then in 2000, a 47 million-year-old anklebone (astragalus) from a four-legged whale was discovered in Pakistan. This bone closely matched the homologous anklebone in an artiodactyl. The biochemists were right, whales are indeed related to hippos and antelopes!

  70. In 2006, a team of scientists, including Edward B. Daeschler, Neil H. Shubin, and Farish A. Jenkins, Jr., unearthed an extinct fossil fish in the Canadian Arctic that dates back to the Devonian Period (360 million years ago). Their discovery appeared in the journal Nature 440 (6 April 2006: 757-763). The fossil fish is named Tiktaalik roseae. This animal has the characteristics of a fish, including gills and scales, but also has the flattened head of a small crocodile and unusual fins used for walking on land. Its fins have thin bones for paddling like most fishes, but they also have sturdy interior bones that would have allowed Tiktaalik to prop itself up in shallow water and use its limbs for support as most four-legged animals do. This remarkable fossil is truly a "missing link," an evolutionary transition between swimming fish and their descendents, a major phylogenetic branch (clade) giving rise to all four-legged vertebrates (tetrapods), including amphibians, dinosaurs, birds, and mammals.

  71. Although cladograms are generated from comparative DNA samples, some are produced repeatedly and have higher "bootstrap" values. Cladograms with the highest bootstrap values are considered the most accurate and reliable. For example, if one thousand cladogram "trees" are generated from a comparative DNA sample and the same pattern comes out 900 times, this cladogram would have a bootstrap value of 90 percent. Evolution is a scientific theory because it is based on an abundance of empirical data, even though the precise mechanisms remain open to tests, revision, and tentative acceptance or rejection. There is substantial factual evidence to show that the genetic makeup of populations changes from generation to generation, and that these genetic changes are reflected in a bewildering array of different species of plants and animals.

  72. A taxonomic group that represents a single branch (clade) in a cladogram, and having a common ancestor, is termed monophyletic. For example, all birds and reptiles are thought to have descended from a single common ancestor and are monophyletic. DNA evidence also indicates that Humans (Homo) and chimpanzees (Pan) are monophyletic. These phylogenetic studies are not always based on an actual "missing link" which may never be found, or has vanished from the fossil record. Cladograms are typically based on detailed computer analysis of the DNA of extant organisms. Cladograms are also based on fossil evidence, particularly in the field of vertebrate paleontology; however, these are sometimes supplemented with evidence from DNA.

     Definitions Of The Terms Monophyletic, Paraphyletic & Polyphyletic 


    13. Monophyletic Groupings: All Descendants From A Common Ancestor

  73. Duckweeds Placed In Arum Family (Araceae) & Genus Acacia Split
    Phylogenetic studies by D.H. Les, et al. (2002), G.W. Rothwell, et al. (2004) and L.I. Cabrera, et al. (2008) indicate that duckweeds belong to the arum family (Araceae). Their cladograms are based on sequences of the trnL-trnF intergenic spacer region of the chloroplast genome. Consequently, the Lemnaceae will no longer appear as a separate family in the latest edition of the Jepson Flora of California. This is especially noteworthy to me since I wrote the section on Lemnaceae for the previous 1993 and 1996 printings! It is interesting to note that duckweeds belong to the same plant family as the titan arum (Amorphophallus titanum). This remarkable plant has a 2.4 m erect spadix that protrudes from a vase-shaped, pleated spathe 4 m in circumference. Many other traditional plant families will also be consolidated as molecular biologists create phylogenetic trees based on consistent monophyletic groupings. Maintaining Lemnaceae and Araceae as distinct families would make the arum family paraphyletic, with a common ancestor but without all of its descendants (i.e. duckweeds are excluded).

     Cladogram For The Arum Family Based On Chloroplast DNA 
    Flow Chart For Duckweed Family Based On Morphologhy

  74. Based on derived characteristics over time, modern phylogenetic trees (cladograms) of animal and plant groupings show all taxa descending from a common ancestor. This grouping is termed monophyletic. Starting with a common ancestor all the branching is typically in 2's (dichotomous), with every new branch (clade) giving rise to a pair of closely related sister clades. Each of these clades in turn gives rise to another pair of sister clades, and so on. Evolutionary relationships displayed in cladograms are not always dichotomous. Three or more branches may arise from a node (polytomy) when closely-related taxa cannot be completely resolved into dichotomies. This is clearly seen in the cladogram for Acacia (see below). In monophyletic groupings all descendants have a common ancestor and share one or more derived characters. See the following simplified cladogram.

    In the above simplified monophyletic cladograms, the grouping depends on the derived characters that the taxa share. A, B, and C are all seed plants because they all share the derived character for seeds that also occurs in the common ancestor. In the above right cladogram, only A & B are truly flowering plants because they share the derived character for flowers that also occurs in their recent common ancester (where A & B arise). This character came later in the evolutionary timeline, so (C) is not a flowering plant.

    A modern representation of the phylogeny of gymnosperms based on chloroplast DNA. Dichotomous (paired) sister branches (clades) with a common ancestor are said to be monophyletic and are more closely related. For example, the conifer division Pinophyta and ginkgo division (Ginkgophyta) have a common ancestor in the cycad division (Cycadophyta). The pine family (Pinaceae) and a sister branch leading to six additional families have a common ancestor within the division Pinophyta. In other words, the seven major families of cone-bearing trees and shrubs all evolved from the division Pinophyta. The araucaria and podocarpus families (Araucariaceae and Podocarpaceae), which have their greatest diversity in the southern hemisphere, are monophyletic and occur side-by-side on sister clades.

  75. Many traditional phylogenetic groupings of species within families and genera are not monophyletic and are inconsistent with modern cladistical analyses based of DNA. In other words, the groupings are paraphyletic or polyphyletic, and do not show all species within a group descending from a common ancestor. Monophyly is the natural evolutionary pattern in which all species are descended from a common ancestor. In order to have consistent computer-generated, monophyletic cladograms, it is sometimes necessary to change paraphyletic and polyphyletic groupings by moving species into different genera, and by moving genera into different families. Many of the taxonomic revisions in the Jepson Manual 2nd Edition (2012) make more sense if you understand the terms monophyletic, paraphyletic and polyphyletic. For example, why was the duckweed family (Lemnaceae) reduced to a subfamily (Lemnoideae) within the arum family (Araceae)? Why were non-phyllode acacias with prickles (e.g. cat's claw acacia) removed from the genus Acacia and placed in a separate genus Senegalia? Hopefully, the following chart will shed some light on these significant changes.

      PCR, Cladistics & Phylogenetic Trees (Cladograms)  

  76. As I stated above, maintaining the duckweeds (Lemnaceae) and arums (Araceae) as distinct families would make the arum family paraphyletic, with a common ancestor but without all of its descendants (i.e. duckweeds are excluded). In order to have a monophyletc, computer-generated cladogram for the arum family, the duckweeds are now placed in the Araceae. Modern reptiles is a paraphyletic grouping that contains a common ancestor, but does not contain all descendants of that ancestor (i.e. birds are excluded). Dinosaurs would also be a paraphyletic grouping because it does not contain the bird descendants.

  77. According to Seigler, D.S., Ebinger, J.E., & J.T. Miller (2006) Phytologia 88 (1): 38-94, morphological and genetic studies indicate that the genus Acacia is polyphyletic with more than one recent ancestor. As shown in the simplified diagram above, the most recent ancestor of "C" is not part of the grouping within the blue square. For example, it has derived traits that are not shared by the recent common ancestor of A & B. Therefore, it cannot be part of the group with A & B. In order to maintain Acacia as a monophyletic genus, "C" must be placed in a different group. If "C" and "D" share the same derived traits and common ancestor, then "C" must be a sister clade with "D." This is essentially why some previous members of the genus Acacia, such as the "cats claw acacia" (Acacia greggii) are now placed in the genus Senegalia. A grouping of warm-blooded animals would include birds and mammals and is called polyphyletic because the members of this group do not include the most recent common ancestor.

    Cat's Claw Acacia Now In Genus Senegalia

  78. Most members of the genus Senegalia differ from Acacia by the presence of prickles and the absence of phyllodes. A naturalized acacia in San Diego County called "sweet acacia" (A. farnesiana var. farnesiana) has been placed in the genus Vachellia. Members of the genus Senegalia can be distinguished from Vachellia by the absence of stipular spines and the presence of prickles. The origin of stipular spines vs. prickles is quite different, and molecular taxonomists have concluded that the separation of these species into separate groups is warranted. Some of the morphological subdivisions in my following Acacia article are now placed in separate genera.

    A. Prickles of cat's claw acacia (Senegalia greggii). B. Stipular spines of sweet acacia (Vachellia farnesiana var. farnesiana). Unlike stipular spines at the bases of leaves, prickles arise from the cortex and epidermis of plant stems. The classic thorns of roses are actually prickles.
    This simplified dichotomous flow chart is not a computer-generated, monophyletc cladogram. It simply shows how the traditional genus Acacia was subdivided into groups in order to key out different species. Some of these species with prickles and stipular spines have been removed from the genus Acacia and placed in new genera. The original 1350 species now comprise 5 genera, with 960 (mostly Australian) spp. still retained in Acacia.

      See Wayne's Word Article On The Genus Acacia  
    Swollen Thorn Acacias & Their Symbiotic Ants
    Vegetative Terms: Spines, Thorns & Prickles

    Computer-generated cladogram of Acacia sensu lato (in the broad sense) showing five major monophyletic lineages (genera) in red. The group containing Mariosousa, Acaciella and Faidherbia is Polytomous. I.e. It doesn't resolve into dichotomies. Faidherbia is a monotypic genus that was formerly classified as Acacia albida. Original cladogram published in: Maslin, Miller & Seigler (2003), Australian Systematic Botany 16 (1): 1-18. The updated generic names follow B.R. Maslin (2006).

      Seach Acacia, Acaciella, Vachellia, Senegalia & Mariosousa in Kew Plant List  
    See Legume (Fabaceae) Subfamilies at the Palomar College Arboretum
    Subfamilies:    Mimosoideae      Papilionoideae      Caesalpinioideae

    Phylogeny of the Rafflesiaceae


    Click on image to see slightly simplified polyphyletic version.


    14. Coexistence Of Grasses & Dinosaurs

  79. The earliest fossils of flowering plants date back approximately 130 million years, to a time when dinosaurs walked the earth. Exactly which ancestral seed plants gave rise to the flowering plants has been a hotly debated topic for more than a century. In fact, in a letter to Joseph Hooker in 1879, Charles Darwin referred to the sudden appearance of flowering plants in the fossil record as "an abominable mystery." Grasses are considered relatively advanced flowering plants, and most macrofossils and pollen from grasses appear long after the demise of dinosaurs at the end of the Cretaceous Period (65 million years ago). Dioramas in museums have long depicted large sauropod dinosaurs grazing on conifers, cycads and ferns in landscapes without grasses. In the November 18 issue of Science, Caroline Strömberg of the Swedish Museum of Natural History and her Indian colleagues Vandana Prasad, Habib Alimohammadian and Ashok Sahni report phytoliths from grasses in the fossilized dung of sauropods that lived in central India about 65 to 71 million years ago.

  80. Phytoliths are microscopic silica bodies found inside the cells of stems and leaves of grasses and other plants. Depending on the species of plant, they range from 5 to 100 micrometers in length. Because they are made of a crystalline form of silica called opal, they are very durable and retain their characteristic shapes over millions of years. Like microscopic pollen grains and diatoms, the phytoliths remain perfectly preserved in spaces between soil particles. Different genera of grasses have phytoliths with unique shapes, including square, rectangular, oblong, bilobed, wavy with undulate margins, and butterfly-shaped. Grasses belonging to the subfamily Panicoideae typically have phytoliths that are shaped like a dumb-bell. I examined the leaf blade of crabgrass (Digitaria sanguinalis), a member of the Panicoideae, and the phytoliths are indeed shaped like a dumb-bell.

    Magnified view of a row of phytoliths within the leaf epidermis of crabgrass (Digitaria sanguinalis). The dumb-bell shaped phytoliths are 32 micrometers in length. Compare this with an average cuboidal grain of table salt in which each side is 300 micrometers long. More than 800 of these crabgrass phytoliths could fit into a box the size of a grain of table salt! Photo taken at 400x and 1000x magnifications with a light microscope.

  81. It is remarkable how much information has been determined about the distant geologic past with new and improved methods of chemical analysis and sophisticated digital instruments. Each day the scientific theory of evolution is becoming more complete, as scientists uncover new facts and piece them together like a complex jigsaw puzzle. DNA, the genetic blueprint of all creatures, provides a stunning, detailed record of evolution, from primitive unicellular bacteria to complex vertebrate animals. This is eloquently described by Sean B. Carroll in his book The Making of the Fittest (2006).

      Phytoliths & Dinosaur Coprolites  
    Grains of Salt & Metric System
    A Comparison Of Cell Sizes


    15. Origin Of The First Land Plants On Earth

  82. Based on fossil evidence and cladistic analysis, the general evolutionary trend for land plants was increasing levels of complexity, from the earliest algal mats, through bryophytes, lycopods and ferns, to the complex gymnosperms and angiosperms of today. Fossil evidence of land plants (embryophytes) is scarce prior to the Silurian Period, although liverwort cryptospores have been found in Argentina dating back to early Ordovician about 470 milion years ago (C.V. Rubinstein, et al. 2010). The spore walls contained sporopollenin, one of the most stable biological polymers known and a characteristic of well-preserved pollen grains throughout the plant kingdom. The earliest land plants were probably similar to liverworts or hornworts with a dominant thalloid gametophyte generation and a reduced sporophyte. Fossils of ancient land plants are well represented in the early Devonian Rhynie Chert beds in Aberdeenshire in the north of Scotland. This time period is approximately 398-416 million years ago, long before the age of dinosaurs. Two of the abundant fossil plants at Rhynie, Horneophyton and Rhynia, are possible relatives of modern day hornworts. These were small, leafless plants only one or two feet tall (30-60cm) with rhizoids instead of true roots. The following statement regarding Horneophyton and Rhynia fossils at Aberdeenshire comes from my old Historial Geology textbook by Carl Dunbar (1960): "The wonderfully preserved plants found there represent almost the simplest possible type of structure a land plant could have, and suggest the steps whereby an aquatic alga adapted itself for land life." This statement has stayed with me all these years and is especially fascinating after studying the relatively simple structure of hornworts and their single large chloroplasts. The lack of any fossil wood prior to the Devonian suggests that this important period of geologic time is when land plants truly colonized the earth. This is truly one of the most important evolutionary breakthroughs in earth's history. It irreversibly changed climates and biogeochemical processes on a global scale, and it enabled eukaryotic life to evolve and invade the continents of the world.

  83. The life cycle and morphology of hornworts (division Anthocerotophyta) has characteristics in common with liverworts and mosses (divisions Marchantiophyta and Bryophyta). In fact, older references reduced all three groups to classes within the division Bryophyta. New evidence from DNA sequencing and cladistic analysis reveals that they represent three distinct divisions (phyla). Unlike mosses and liverworts, the hornwort sporophyte continues to grow throughout its life from a meristematic region near the base and not from the tip as in other plants. Unlike liverworts, most hornworts have true stomata on their sporophytes as in mosses. The slender, erect sporophyte has a multicellular outer layer, a central rod-like columella, and a layer of tissue in between that produces meiospores and pseudoelaters. At maturity the sporophyte splits open just below the apex to release the spores inside. This dehiscent region containing spores is essentially a sporangium. The pseudoelaters are multicellular, unlike the elaters of liverworts. Helical thickenings cause the pseudoelaters to change shape and twist as they dry out, thereby helping to disperse the mass of trilete spores. When trilete spores separate from the common tetrad, each spore shows 3 lines radiating from a central pole. In monolete spores there is a single line on the spore surface indicating that the mother cell split into 4 along a vertical axis. The early nonvascular land plant Horneophyton also had a central columella and trilete spores.

  84. Like liverworts, the haploid gametophyte (thallus) of hornworts is dorsiventrally flattened. It often becomes slimy due to mucilage-filled cavities when groups of cells break down. These cavities are invaded by colonies of cyanobacteria (Nostoc) giving the thallus a blue-green color. One of the most unusual characteristics is the single large chloroplast per cell. A single chloroplast is common in green algae (division Chlorophyta) but it is quite uncommon and unusual for true multicellular plants (kingdom Plantae). Like mosses and liverworts the motile sperm are biflagellate and swim to the egg via water. Cladistic analyses suggest that hornworts (Anthocerotophyta) originated much earlier in the history of land plants, possibly before the Devonian. Hornworts may even be one of the earliest lineages of land plants. Some of their morphological characteristics are similar to sporophytes of the ancient land plant Horneophyton that lacked true vascular tissue. In fact, some paleobotanists have suggested that Horneophyton may be the "missing link" between hornworts and the Rhyniopsida, an extinct class of early vascular plants that includes Rhynia. Some of these characteristics are shown in the following image.

    A hornwort compared with the extinct 400 million-year-old land plants Horneophyton and Rhynia.

    Moss Life Cycle Has Animal-Mediated Fertilization!

    Mosses belong to the division Bryophyta characterized by nonvascular plants with embryos that develop within multicellular female sex organs called archegonia. The dominant (conspicuous) part of the life cycle is the haploid, leafy gametophyte. The diploid sporophyte consists of a sporangium-bearing stalk that grows directly out of the gametophyte. Spore mother cells within the sporangium undergo meiosis, producing numerous haploid spores that fall to the ground like tiny particles of dust. Since the sporophyte is without chlorophyll, it is completely dependent on the autotrophic (photosynthetic) gametophyte for its water, minerals and carbohydrate nutrition. Consequently, the sporophyte of the moss is heterotrophic and parasitic on the gametophyte. About half of all moss gametophytes are dioecious, with separate male and female individuals in the population. The gametophytes are produced by "male" and "female" spores. Mosses have a primitive method of fertilization that involves a motile, biflagellate sperm that swims through water to reach the egg on female plants.

    For more than a century, textbooks stated that moss sperm needed water to swim or splash to a female archegonium. According to Lils Cronberg and his colleagues at Lund University, Sweden (2006), mosses have a carrier system for sperm that is similar to pollen transfer in flowering plants. This explains how moss plants spaced too far apart for swimming sperm produce sporophytes following fertilization. From a simple lab experiment it has now been shown that fertile moss shoots attract minute arthropods (collembolans and mites) that passively carry moss sperm, similar to bees with pollen in flowering plants. The role of collembolans in moss fertilization is undoubtedly much older due to the antiquity of mosses. Mosses and collembolans are extant members of ancient organisms that originated and radiated after the early colonization of land about 440-470 million years ago.

  85. Collembola are also known as springtails because they have a forked springing device or furcula at their posterior end. It is folded beneath the tail under tension which can be released suddenly, catapulting the springtail into the air and hopefully out of harm's way. They are classified as hexapods along with insects; however, DNA analysis has shown that they do not belong to the class Insecta. They represent a separate evolutionary line (class) that includes Protura and Diplura. They are considered the most abundant hexapod on earth with over 6,000 known species. In just one handful of grassland soil there can be literally thousands of individuals representing hundreds of different species. They feed primarily on detritus and microscopic life, including fungal hyphae, bacteria and algal cells. Along with nematodes, collembola are one of the main biocontrol agents on microbial populations. There are also parasitic species associated with dermatitis in humans. One of the most interesting collembola are called "snow fleas" (Achorutes nivicolus) that feed on the unicellular alga (Chlamydomonas nivalis) that colors the snow red.

    Left: Snow fleas (Achorutes nivicolus) in the hexapod class Collembola. Center: A boot print in pink snow. Right: Bright red resting cells (aplanospores) of snow algae (Chlamydomonas nivalis) and a pine pollen grain. Snow fleas can jump by means of a springing device or furcula (red arrow). Unlike other colorless soil springtails (see below), snow fleas are dark-colored. This allows them to absorb heat from the sun. They also produce a glycine-rich protein that works like anti-freeze, allowing them to function in sub-zero environments.
    Left: Soil springtails compared with the "eye" of an ordinary sewing needle. They are actually colorless and about 1.0 to 1.5 mm long; however, backlighting makes them appear darker. With their springing device or furcula they can jump about 100 times their body length or about 7-8 inches (18-20 cm). Although they are abundant in some soils, they are barely visible with the naked eye. In just one handful of grassland soil there can be literally thousands of individuals representing hundreds of different species.
    Left: Magnified view of a soil springtail taken with a Bausch & Lomb dissecting microscope and Sony W-300 camera. The springing device (furcula) is clearly visible on the ventral side of posterior end. A handful of soil can contain literally hundreds (or thousands) of springtails. Because of their small size and colorless bodies they are difficult to see with the naked eye. In order to acheive a more accurate rendition of its colorless body, I used backlighting and then "invert" with Adobe Photoshop.


    16. Origin Of Flowering Plants (Angiosperms)

  86. Although considerable evidence has been compiled since the time of Darwin, the precise origin of flowering plants in the early Cretaceous (140 million years ago) remains an enigma. As I stated above, Darwin mentioned this controversy in 1879 when he referred to the origin of flowering plants as an "abominable mystery." There are at least four hypotheses to explain the origin of flowering plants.

    The following cladograms illustrate four different hypotheses for the origin of flowering plants. They show common ancestry between angiosperms and more ancient gymnospermous groups, including cycads, gnetophytes and other conifers. A. According to the Anthophyte Hypothesis, Gnetophyta (Mormon tea & allies) and angiosperms are monophyletic and share a common ancestor. This is based (in part) on the presence of vessels and double fertilization in some gnetophtyes. B. According to the Gnetifer Hypothesis, gnetophytes are most closely related to other conifers and not angiosperms. C. In the Gnepine Hypothesis, gnetophyes are monophyletic with the pine family Pinaceae. D. The Cycad Hypothesis has angiosperms monophyletc with cycads. The latter hypothesis is based (in part) on the superficial resemblance of a female "cone" of Cycas revoluta to a large angiosperm flower. See flowerlike "cone" of female Cycas revoluta in image to the right.


    Cladograms showing four different hypotheses for the monophyletic origin of flowering plants.

    Molecular phylogenetic studies indicate that the first split within modern angiosperms is between a lineage that includes a single species (Amborella trichopoda) and all the rest of the extant angiosperm species. In other words, Amborella is monophyletic with all the rest of the angiosperms (see right cladogram: Origin of Amborella & Angiosperms). Amborella trichopoda is a rare flowering shrub that grows in the rain forest understory in New Caledonia. Unlike practially all other angiosperms, Amborella xylem has only tracheids, supporting the modern view that the first angiosperms lacked vessels. Amborella gametophytes are also unusual in having three, rather than two, synergid cells with the egg cell at the micropylar end (egg apparatus), hence a total of nine nuclei and eight cells in the embryo sac. According to W.E. Friedman (Nature 441, 2006), this extra cell in the egg apparatus could provide evidence of a critical link to the gymnospermous ancestors of flowering plants. The gametophyte of the vast majority of angiosperms has three cells in the egg apparatus, and a total of seven cells and eight nuclei in the embryo sac (see angiosperm life cycle below).
    Origin of Amborella & Angiosperms.

    Underside of flowering branch of male Amborella trichopoda.

    Close-up view of male (staminate) flowers of Amborella trichopoda. Each flower is aprroximately 4 to 5 mm in diameter with a dozen or more bract-like tepals (perianth segments undifferentiated into petals & sepals). The flowers have a dozen or more spirally arranged stamens, which become progressively smaller toward the center.


    Water Lily (Nyphaea odorata)
    Amborella trichopoda (above): A rare, sprawling, understory shrub from New Caledonia, and the most primitive living flowering plant. It belongs to the monotypic family Amborellaceae in the monotypic order Amborellales. Most authorities consider it to be the living descendent of a line of primitive flowering plants without vessels that diverged near the base of the main clade of vessel-bearing angiosperms about 130 million years ago. The younger growth (inset) has bright green, shiny leaves. The flowers have many tepals (perianth parts not differentiated into calyx & corolla) and numerous stamens. They are similar in appearance to miniature versions of the closely-related water lily clade (order Nymphaeales), see left image.
    1. Williams, J.H. 2009. "Amborella trichopoda (Aborellaceae) and the Evolutionary Developmental Origins of the Angiosperm in Programic Phase." American Journal of Botany 96: 144-165.

    Left: Vessels in midvein of petal from Brodiaea terrestris ssp. kernensis. The spirally-thickened secondary cell walls appear like coiled springs. This provides strength as well as flexibility to these strands of tubular, water-conducting cells that compose the xylem (vascular) tissue. Right: Two types of water-conducting cells: tracheid and vessel (vessel element). Technically a vessel is composed of many hollow vessel elements joined end-to-end like sections of PVC pipe. With the exception of the Gnetophyta, most gymnosperms lack vessels. Vessels are characteristic of all flowering plants, except for the earliest ancestral sister clade (Amborella) that have only tracheids like most gymnosperms.


    17. The Remarkable Angiosperm Life Cycle

  87. From their first appearance in the fossil record of early Cretaceous, flowering plants evolved into the dominant land plants on earth in a relatively short period on the geologic time scale. There are a number of tentative hypotheses to explain this astonishing explosion of species. Did the development of vessels and vascularization of leaves with more efficient water conduction systems give them a significant photosynthetic advantage? Perhaps pollination & fertilization followed by seed and fruit development is more efficient in flowering plants. The evolution and diversity of flowering plants certainly coincides with amazing insect diversity. When flowering plants began to dominate the landscape, they edged out the conifers, tree ferns and cycads that the long-established sauropod dinosaurs depended on. The competitive advantage of flowering plants is probably a lot more complicated, and undoubtedly is related to changing climatic conditions (and perhaps an enormous asteroid that collided with the earth causing a global dust cloud that blotted out the sun for months). At any rate, flowering plants possessed many adaptive traits that made them particularly resistant to drought and extreme cold. Some of these sophisticated advancements included more efficient water-conducting cells, advanced photosynthetic patterns adapted to drought conditions, including C4 and CAM photosynthesis, advanced leaf and stem anatomy that could withstand environmental extremes, cold and drought-deciduous foliage (which is rather uncommon in today's gymnosperms), perennials with dormant underground rootstocks capable of surviving severe winters, extremely tough, resistant seed coats that protect the dormant embryo inside for prolonged unfavorable periods, an enormous chemical defense arsenal against disease organisms and herbivores, and an efficient pollination and dispersal system involving complex interactions with animals. Flowering plants have literally colonized every conceivable habitat on earth, including the extensive fast-growing, fire-adapted grasslands of today that support huge herds of grazing mammals, and yet many of these vast vegetation types were not around when dinosaurs reached their peak.

    Typical angiosperm life cycle: Flowering plants (angiosperms) belong to the vascular plant division Anthophyta. Like ferns and conifers, the diploid sporophyte consists of a herbaceous or woody plant with roots, stems and leaves. Unlike ferns and conifers, flowering plants produce reproductive organs called flowers and seed-bearing fruits. The term angiosperm is derived from angio (vessel-like container) and sperm (seed), referring to the seed-bearing containers called fruits. The female gametophyte of Amborella is very unusual because it has three synergid cells rather than the usual two found in most angiosperms. In addition, the typical water conducting cells called vessel elements (vessels) found in practically all flowering plants are absent in Amborella. The variation in size, color, number and arrangement of floral parts in blossoms of the 300,000 different plant families is absolutely staggering.



    silver sword
          18.  Adaptive Radiation On The
            Hawaiian & Galapagos Archipelagos

    alula

  88. The Hawaiian archipelago has been isolated from continental land masses during the past 30 million years, and yet the 1,000 species of indigenous Hawaiian angiosperms are believed to stem from natural introduction by long-distance dispersal of 280 ancestral plant colonists (Manual of the Flowering Plants of Hawaii by Wagner, W.L., Herbst, D.R. and S.H. Sohmer, 1990). It appears that seeds were carried thousands of miles to these islands, possibly by rafting or within protective capsules and pods. For example, an ancestral California tarweed of the sunflower family (Asteraceae) traveled at least 3,000 miles to the Hawaiian Islands where it gave rise to a remarkable group of endemics known as the "Silver Sword Alliance." The small seeds from ancestral members of the lobelia family (Campanulaceae) also reached these islands from the American mainland giving rise to an unusual group of endemic Hawaiian lobelioids. This phenomenon where ancestral species colonize a new habitat and evolve into different species is called adaptive radiation. The new species evolve in response to different selection pressures that enable them to fill unique ecological niches. The story of Darwin's Finches on the Galapagos Islands is a classic example of adaptive radiation. The Hawaiian silver swords and lobelioids are truly unusual in appearance. They are strikingly different in appearance compared with California tarweeds or members of the lobelia family on the mainland of North and South America. Their taxonomic affinities with ancestral species are based on chromosome comparisons, hybridization studies and comparative chloroplast DNA. The unscientific hypothesis that these bizarre plants were placed here in their present form by a creator is untenable.

    Alula (Brighamia insignis), a rare member of the lobelia family (Campanulaceae) endemic to steep sea cliffs on the island of Kauai. Alula is perfectly adapted for living on vertical volcanic cliffs. A single rosette of leaves arises from the top of a thick, succulent stem, like a cabbage head on a baseball bat. The rosette varies in size, depending on the availability of moisture. Roots penetrate the cliffs horizontally, and the base of the plant is rounded, permitting the plant to rock slightly in the wind. Water stored in the stem enables the plant to survive periods of drought which may last days or weeks. The flower is very different from members of the lobelia family on the mainland of North America. Another rare species with white flowers (B. rockii) grows on sea cliffs along the windward coast of Molokai. Like Hawaii's endemic silver sword alliance that evolved from an ancestral tarweed (Asteraceae), the alulu is another example of adaptive radiation. According to Sherwin Carlquist (Hawaii: A Natural History, 1980), the Hawaiian lobeliads evolved from several ancestral introductions rather than a single original colonization; however, molecular data from Thomas J. Givnish of the University of Wisconsin (Evolution on Islands, 1998) indicate that they are monophyletic in origin and represent the product of a single introduction.

    18. Adaptive Radiation On The Galapagos Archipelago

    Giant prickly pear cactus (Opuntia echios var. gigantea) on Santa Cruz Island and Galapagos marine iguana (Amblyrhynchus cristatus) on Hood Island. The remarkable giant Galapagos prickly pear evolved a tall woody trunk resembling a ponderosa pine to protect it from browsing by giant tortoises. The marine iguana is unique amoung modern lizards because it dives and forages in the sea. There are also endemic land iguanas on the Galapagos Islands that feed on prickly pear cactus and other vegetation. These are excellent examples of adaptive radiation where ancestral species colonized a new habitat and evolved into different species. Many thousands of years ago, cactus and iguanas floated out to these volcanic islands from the mainland of Ecuador on rafts of debris. The new species evolved in response to different selection pressures that enabled them to fill unique ecological niches. The story of Darwin's Finches on the Galapagos Islands is another classic example of adaptive radiation.


    19. Homoplasy: Parallel & Convergent Evolution

    A small mantispid and a preying mantis. Although they differ greatly in size, these two insects are remarkably similar in appearance. They both have triangular heads with large eyes and a pair of raptorial (grasping) front legs. Their other two pairs of legs are used for walking. They belong to two very different insect orders. Although mantids were once placed in the order Orthoptera along with grasshoppers, crickets and cockroaches, they are now placed in the separate order Mantodea. Mantispids belong to the order Neuroptera, along with lacewings, snakeflies and antlions. Their remarkable adaptive similarity is an example of convergent evolution.

  89. Sometimes evolutionary change follows a common pathway in two or more unrelated or distantly-related organisms because of similar environmental pressures. It culminates in unrelated organisms with similar morphological characteristics even though they did not have a common ancestor. This phenomenon is called parallel evolution. There are many examples of parallel evolution in plants, including distantly-related plant families that have evolved from an autotrophic to a parasitic mode of existence. Some plants have evolved independently into a mycotrophic mode of existence where they obtain nutrients from mycorrhizal soil fungi, which in turn, are parasitic on the roots of nearby forest trees and shrubs. Photosynthetic pathways, such as CAM (crassulacean acid metabolism) and C-4 photosynthesis, have also evolved independently in distantly-related plant families.

  90. Another example of parallel evolution is the appearance of xylem vessels in the vascular tissues of very distantly-related plants, such as Ephedra in the gymnospermous division Gnetophyta and flowering plants in the angiospermous division Anthophyta (Magnoliophyta). In addition, species of Ephedra have double fertilization, where two sperm are involved in the fertilization process. Double fertilization was once thought to be a strictly angiosperm characteristic. Some older references have suggested that the Gnetophyta may represent a "missing link" in the evolution of flowering plants, but others say that vessels and double fertilization are examples of parallel evolution, and the Gnetophyta are more closely related to conifers than angiosperms. The current consensus among authorities (as of 2010) is that Amborella trichopoda (a primitive angiosperm without vessels) and all other flowering plants represent sister clades derived from an common ancester without vessels. This latter conclusion supports the independent (parallel) evolution of vessels in the Gnetophyta.

    Left: Ephedra viridis in the Panamint Range overlooking Death Valley National Monument. Right: Wildflowers in Anza-Borrego Desert State Park. Although Ephedra belongs to an entirely different plant division (Gnetophyta), it has several characteristics of flowering plants (division Anthophyta) including vessels and double fertilization. These traits are considered to be homoplastic because they evolved independently through parallel evolution in distantly related ancestors. Some authors would call this convergent evolution. If Ephedra and flowering plants shared a common ancestor with vessels and double fertilization, the appearance of these traits would not be an example of parallel evolution. [Wildflowers include Encelia farinosa, Cylindropuntia bigelovii, Lupinus arizonicus and Mimulus bigelovii.]

  91. The laurel family (Lauraceae) includes about 2,000 species of trees and shrubs in 50 genera. Familiar genera in the family include Cinnamomum (cinnamon and camphor), Laurus (European bay), Umbellularia (California bay), Sassafras and Persea (avocado). One genus in this family (Cassytha) has broken away from the other trees and shrubs and has evolved into a leafless, twining parasitic herb that absorbs nutrients from it host by a specialized modified root called a haustorium. The distantly-related morning-glory family (Convolvulaceae) also has about 50 genera of trees, shrubs and vines. Like the laurel family, one of these genera (Cuscuta) has evolved into a twining, leafless parasitic herb with a specialized organ of absorption (haustorium). Some botanists place this genus in its own family, the Cuscutaceae, although the floral morphology is very similar to some members of the Convolvulaceae. Both Cassytha and Cuscuta are remarkably similar in appearance, even though they live in different parts of the world and do not share a common ancestor. The radical modification of these two unrelated plants into specialized parasites is a marvelous example of parallel evolution, or convergent evolution if you prefer the latter term.

    Left: Cassytha filiformis (Lauraceae) on the Caribbean Island of Grand Cayman. Right: Cuscuta californica (Convolvulaceae or Cuscutaceae). These twining, parasitic plants are without chlorophyll and absorb nutrients from their host plants be means of specialized roots called haustoria.

  92. When parallel evolution under similar environmental conditions in distantly-related organisms results in plants and animals that are morphologically very similar in overall appearance, this is usually called convergent evolution. It should be noted here that some authors use these two terms interchangeably. North American cactuses (family Cactaceae) and South African euphorbias (family Euphorbiaceae) belong to different plant families and are distant relatives in the phylogeny of flowering plants; however, they both have succulent, thick stems that store water, they both have spines for protection, and the both are adapted for survival in arid desert regions with low rainfall. Without flowers, some African euphorbias are practically indistinguishable from their North American counterparts.

    Homoplasy: Which of these xerophytes is a cactus and which one is a euphorbia?

  93. The supplemental biology text Of Pandas and People (2nd. Edition, 2004) that is endorsed by advocates of intelligent design includes a different definition for parallel evolution. According to the authors of the latter text, "If two organisms are judged to be related through a "recent" common ancestor, their similarities are said to result from parallel evolution." They also state that if the ancestor is distantly related, convergent evolution has occurred. This definition of parallel evolution is incorrect. In parallel evolution, the two organisms don't necessarily share a common ancestor; however they do experience similar kinds of environmental pressures and survive by developing similar adaptations.

    Why Differentiate Parallel From Convergent Evolution?

  94. The following paragraph is from an article by Jeff Arendt and David Reznick in Trends in Ecology and Evolution Vol. 23 (1): 26-32, 2007:

      "Biologists often distinguish 'convergent' from 'parallel' evolution. This distinction usually assumes that when a given phenotype evolves, the underlying genetic mechanisms are different in distantly related species (convergent) but similar in closely related species (parallel). However, several examples show that the same phenotype might evolve among populations within a species by changes in different genes. Conversely, similar phenotypes might evolve in distantly related species by changes in the same gene. We thus argue that the distinction between 'convergent' and 'parallel' evolution is a false dichotomy, at best representing ends of a continuum. We can simplify our vocabulary; all instances of the independent evolution of a given phenotype can be described with a single term - convergent."

      "If the use of the terms 'parallelism' and 'convergence' cannot be associated with a clear dichotomy, either at a phylogenetic level or a molecular level, then their continued use is not justified and can even be misleading. They are relics of a time when we could not evaluate the underlying causes of phenotypic similarity and were confined to inferences based on comparative anatomy. These terms are also relics of a time when there was not an appreciation of the complexity of genetic and developmental networks that underlie the determination of simple phenotypic traits, such as coloration. We argue that this might be a good time to simplify our vocabulary. We need only one term to describe the independent evolution of phenotypic similarity. 'Convergent evolution' will do nicely."

  95. In Australia there are many examples of marsupials that resemble our North American placental mammals. For example, Australia's flying phalanger is remarkably similar to the North American flying squirrel. Both tree-dwelling mammals glide through the air with their parachute-like fold of furry skin between the front and hind legs. These are excellent examples of convergent evolution.

    Homology: Similarity Of Characteristics Due To Origin From A Common Ancestor.
    Homoplasy: Similarity Due To Independent Origin From Distantly Related Ancestors

  96. I prefer to use the terms homology and homoplasy when dicussing the evolution of similar characteristics. Homology refers to similarity due to a common ancestor. Characteristics derived from a common ancestor are termed homologous. Homologous organs are similar in structure and embryonic origin but are not necessarily similar in function. Cactus spines are homologous to bud scales of an axillary bud. Seed-bearing carpels of flowering plants are homologous to leaves because of their similarity in form, anatomy and development. The bone structure in the wings of a bat is homologous to the forelimbs of humans and other mammals. For example, a bat's wing and whale's flipper both originated from the forelimbs of early mammalian ancestors, but they have undergone different evolutionary modification to perform radically different tasks of flying and swimming. The presence of homology is evidence that organisms are related.

  97. Homoplasy (ho-MOP-la-see) means similarity due to independent origin that is not from a common ancestor. Using the term homoplasy avoids the confusing distinction between parallel and convergent evolution. Homoplastic characteristics, such as the spines of cacti and stem-succulent euphorbias, evolved independently from each other. Cactus spines arise from an axillary growth center called an areole. Euphorbia spines are derived from modified stipules. Homoplasy includes parallel and convergent evolution. Similarity of appearance in unrelated or distantly-related organisms is often the result of similar evolutionary pathways under similar environmental conditions. For example, the wings of birds and insects are used for flight. They are analogous but not homologous because their structure, embryonic development and genetics is very different. In addition, they do not have a common ancestral origin at the beginning of their evolutionary development. Sometimes it is unclear whether similarities in structure in different organisms are analogous or homologous. For example, the wings of birds and bats are homologous in that they are both modifications of the forelimb bone structure of early reptiles. However, bird's wings differ from those of bats in the number of digits and in having feathers for flight while bats have no feathers. Bat wings involve the bones that in humans make up the hands, while bird wings lack many of these bones entirely, and instead include only the bones that in humans make up the arms. In addition, the power of flight arose independently in these two very different classes of vertebrates. The two lineages had a long evolutionary separation before they independently became fliers. Wings in birds evolved from early reptiles, and in bats they evolved after their mammalian ancestors had already completely differentiated from reptiles. Thus, the wings of birds and bats can be viewed as analogous rather than homologous upon a more rigorous scrutiny of their morphological differences and evolutionary origins.

  98. Homoplasy is a characteristic shared by members of a phylogenetic tree (cladogram), but not present in their nearest common ancestor. It arises independently by convergent evolution in more than one clade. For example, both mammals and birds are able to maintain a high constant body temperature (warm-blooded). However, the ancestors of each group did not share this character, so it must have evolved independently. Mammals and birds should not be grouped together on the basis of whether they are warm-blooded.

    A. Equisetum (Division Sphenophyta). B. Casuarina (Division Anthophyta). Two unrelated plants in different divisions of the plant kingdom. They both have jointed stems with whorls of scale-like leaves at the nodes. One is a flowering tree and the other is a non-flowering plant with an apical spore-bearing cone (strobilus). Is this an example of homology or homoplasy?

    A hummingbird and hawkmoth, a classic example of convergent evolution (homoplasy). These two distantly related animals are adapted to hovering over flowers and sipping nectar with their long tongues. The hummingbird sips sugary nectar from the tubular flowers of the Mexican coral tree (Erythrina coralloides). As the hummingbird feeds, pollen adheres to its head and bill and is transferred from one flower to another. If the pollen is transferred between flowers of different trees, then cross pollination is accomplished. The tree supplies the hummingbird with sucrose-rich nectar for this valuable pollination service. The nocturmal hawkmoth (Manduca sexta) has a long proboscis which reaches the nectar in long, tubular flowers of jimsonweed (Datura) and Petunia species.

  99. Another example of homoplasy is the evolution of similar glistening bodies in the flowers of distantly related plant families. According to Peter K. Endress (Diversity and Evolutionary Biology of Tropical Flowers, Cambridge University Press, 1994), some flowers display glistening bodies to attract insects. They are interpreted as mimicking nectar drops. They are best known in the temperate genus Parnassia (Saxafragaceae), where they have been termed "pseudonactaries." Similar structures also occur in genera of tropical and subtropical regions, such as Solanum (Solanaceae), Lopezia (Onagraceae) and Nemacladus (Campanulaceae). Although their origin and morphology may be different, they appear to have the same function. They are completely dry, and there is no sign of secretory activity; however, they are often situated near the real nectaries, which are in a more hidden position. Pollinators may be led to the nectar source by these pseudonectaries. "The gadgets of Nemacladus are bizarre. Two stamens have a protruding socket at the filament base. Each socket bears three or more reflexed clavate giant cells, which cause the glistening effect."

  100. Aaron Schusteff (personal communication, 2012) photographed insects from three different families (two bee flies and a wasp) on three different species of Nemacladus. See thumbnail images at the following link: Schusteff Images. Two of the visitors (the bee fly Lepidanthrax and a chalcid wasp) were apparently taking nectar. A second bee fly (Mythicomya) spent most of its time probing the anthers and stigma of N. rubescens. According to Schusteff: "It seems plausible to me that they all may have been attracted by glistening of the rods...simulating well-charged nectaries."

    Left: Nemacladus rubescens of the bellflower family (Campanulaceae). Right: Magnified view of translucent, glistening cells attached at base of filaments on upper side of gynoecium. These cells may serve to attract insect pollinators like "pseudonectaries" in the saxifrage family (Saxifragaceae).

  101. The recently discovered cerambycid beetle Onychocerus albitarsis in Peru is truly one of the most remarkable examples of convergent evolution (homoplasy). It is described by A. Berkov, N. Rodriguez and P. Centeno in Naturwissenschaften Vol. 95, March 2008. Venom-injecting structures have arisen independently in unrelated arthropods, including spiders, centipedes and antlions. The venom is injected through hollow fangs (poison jaws), or in the case of centipedes, through modified forelegs. Among insects only wasps, bees and ants of the order Hymenoptera are known to possess true stingers. Microscopic examination of the newly discovered beetle has revealed that the tip of each antenna is truly a stinging device. In fact, Mr. Centeno discovered this fact first hand. As he grabbed the beetle, the insect jerked back its antennae and pricked his finger, which swelled as if stung by a bee. This is the first example of a stinger in the enormous beetle order Coleoptera.

    A hypothetical cladogram showing the origin of a similar stinging device in two distantly related groups of arthropods that is not present in their nearest common ancestor. These stinging organs are not homologous. Although they are remarkably similar in appearance and function, they are structurally quite different. One is the modified terminal segment of a tail, and the other is from the terminal segment of a beetle antenna.

  102. The terminal antennal segment of Onychocerus albitarsis has two pores opening into channels leading to the pointed tip through which the venom is delivered. The delivery system is almost identical to that found in the stinger of certain scorpions. Since beetles and scorpions belong to entirely different arthropod orders and are only distantly related, this is a dramatic example of homoplasy: similarity due to independent origin that is not from a common ancestor. In this case the homoplastic characteristics (stinging devices) evolved independently from each other. Although the article in Naturwissenschaften uses the term "convergent evolution," one might argue that this is "parallel evolution." The term homoplasy makes this confusing distinction unnecessary.

    Tail of Arizona desert scorpion (Hadrurus arizonensis)
    Beetles, Stinging Organs,
    and Fang-Like Jaws




    20. Homoplasy: Carrion Flowers That Attract Flies & Beetles For Pollination

  103. Some of the world's largest and truly bizarre flowers emit odors that attract flies and beetles. They are often called "carrion flowers" because they have the overpowering scent of rotting flesh or excrement. Some even have the color and harriness of a dead animal. Blow flies lay their eggs in the flowers, but the maggots often perish without a food supply. They belong to a variety of distantly related families and are quite different from each other based on morphology and DNA. Since they have evolved independently they are excellent examples of convergent evolution, specifically homoplasy. I have dedicated an entire page to these remarkable flowers at the following link on Wayne's Word.

    The remarkable starfish flower (Stapelia gigantea), a member of the family Apocynaceae (subfamily Asclepiadoideae). The carrion stench attracts green bottle flies of the blowfly family Calliphoridae. The flies have laid small white eggs on the hairy flower surface; however, there is no hope of survival for the tiny maggots that will soon hatch. Although the flower gives off the exact odor of rotting flesh, it provides no food for the blowfly larvae. The benefit of this clever carrion masquerqade to the flower is pollination by blowflies, ideally from another starfish plant.

    Three unrelated families of flowering plants all with bizarre flowers that emit the scent of carrion. Rafflesia arnoldii is a parasitic flowering plant native to Sumatra. It lives inside the stem of its host vine, only breaking through the stem surface as a large bud when it is time to flower. Hydnora africana is a root parasite on shrubby species of Euphorbia in South Africa. The Malaysian-Indonesian) Amorphophallus titanum grows from an enorous tuber up to 6 feet (2 m) in circumference and weighing up to 120 pounds (54 kg). The massive "flower" is technically an inflorescence composed of numerous small, unisexual male and female flowers. The minute flowers are clustered around the base of the erect spadix, within the showy, vase-shaped, pleated spathe. The 8 foot phallus-like spadix of A. titanum rivals the size of a blue whale penis. It is sometimes called the "stinking corpse lily," although this descriptive common name is more commonly applied to Rafflesia arnoldii.

  104. Flower "scent mimics" that lure carrion insects into their putrid blossoms are some of nature's most fascinating and successful experiments in evolution. They certainly represent some of the most fantastic examples of floral diversity. Although they include some of the largest and showiest blossoms in the world, they will probably never be used in a floral arrangement on your dining room table.


    21. Origin Of Eyes In Distantly Related Animals: Is This An Example of Homoplasy?

  105. In Chapter 6 of The Origin of Species, Charles Darwin expressed concern over how a complex organ, such as the eye, could evolve by natural selection. "... if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real." In fact, some creationists have taken the previous quotation out of context and used it in their argument against evolution be means of natural selection. Like the wings of birds, bats and insects, many biologists have used the term homoplasy to explain the independent origin of eyes in diverse groups of animals. In fact, because the anatomy of the camera-like vertebrate eye is so different from the simple eyes of limpets and the compound eyes of insects, scientists thought that eyes evolved independently numerous times.

  106. Homoplasy may not adequately explain the origin of eyes in different animal phyla. Recent evidence indicates that eye-forming genes evolved only once in a distant ancestor. These primordial eye genes provided the ancestor of present-day animals with photoreceptor cells and the ability to detect light. Mutations and evolution brought other genes under the control of these primordial genes, and together they produced a variety of eyes from simple to complex. With photoreceptor cells at the base of a simple eye cavity, mutations and modifications leading to a more advanced eye are plausible. An explanation for the development of eyes in different present-day species of mollusks is presented by M.F. Land and D.-E. Nilsson (2002) in their book Animal Eyes. This fascinating hypothesis is summarized by C. Zimmer in the November 2006 National Geographic.

    Three examples of mollusks in the diverse phylum Mollusca.

  107. All of the following mollusks share a common ancestral trait: A layer of light-sensitive cells at the base of an eye cavity. In the limpet, this layer of photosensitive cells in a shallow depression can detect light but the eye cannot produce an image. Beyrich's slit shell has a deeper eyecup that provides more information about the direction of the light source, but creates no image. In the chambered nautilis, a small gap at the top of the eye cavity acts as a pinhole pupil, focusing light on photosensitive cells that serve as a rudimentary retina. In Murex, fluid in a fully enclosed eye cavity functions as a primitive lens, focusing light on the retina to create a slightly sharper image. In the common octopus, advanced vision is created by a more complex eye equipped with a protective cornea, colored iris, and focusing lens.

    Light Gathering Propeties Of The Barn Owl

    The barn owl (Tito alba) is remarkably adapted for night vision. The large, forward-facing eyes give owls the best stereoscopic (3D) vision of all birds. This is essential for judging distances, particularly when diving to catch small rodents on the ground. Because of their tubular shape, the eyes are in a fixed position; therefore, the owl must move its head rather than its eyes. In fact, some owls can rotate their head almost 270 degrees in either direction. The beak is positioned relatively low on the face, keeping out of the owl's field of view. The retina is very large compared with other birds and is packed full of light sensitive rods, about 56,000 per square mm in the Tawny Owl (Strix aluco). These rods are far more sensitive than cones at low light levels. According to World Owl Trust: "Tawny Owls would appear to have the best developed eyes of all owls, indeed of all vertebrates, being probably about 100 times more sensitive at low light levels than our own." The phenomenal light gathering properties of the owl are further enhanced by the large, reflective, mirror-like layer (tapetum lucidum) behind the retina. Even though my camera was about 75 feet away, this reflective layer glows in the flash image, a phenomenon known as eyeshine.


    22. Punctuated Equilibrium & Natural Selection

  108. The term evolution is very broad and has numerous subdivisions, particularly explanations for the mechanisms of change. Charles Darwin's On the Origin of Species by Means of Natural Selection was a testable scientific hypothesis that explained one mechanism of evolution called natural selection. Alfred R. Wallace also came up with this hypothesis at the same time period (see "The Man Who Wasn't Darwin" by David Quammen in December 2008 National Geographic). In fact, Darwin and Wallace coauthored a paper on natural selection for Journal of the Proceedings of the Linnean Society in 1858. The following year, Darwin published his Origin of Species and his name is usually associated with the theory of evolution. Natural selection may explain some aspects of evolution; however, there are other explanations. In the first edition of Origin of Species, Darwin was careful to acknowledge the limits of natural selection, writing, "I am convinced that natural selection has been the main but not the exclusive means of modification." Nevertheless, he was misinterpreted as claiming that natural selection was entirely responsible for evolution. In fact, evolution and natural selection have been used interchangeably by some authors. Other scientific hypotheses to explain certain mechanisms of evolution include punctuated equilibrium and symbiogenesis. Punctuated equilibrium was proposed by Niles Eldredge and Steven Jay Gould in the 1970s. It postulates that speciation may occur relatively quickly in geologic time, with long periods of little change (equilibria) in between. Punctuated equilibrium explains the evolutionary patterns of species as observed in the fossil record, particularly the sudden appearance of new species in a geologically short period of time.

  109. In his book On Naval Timber and Arboriculture (1831), Patrick Matthew gives precisely the same view as Darwin and Wallace on the origin of species by natural selection. His main premise was that Britain's navy needed sturdy ships made from first-class timber: Nurserymen's artificial selection of seeds would eventually result in varieties that would not survive well in the wild, thus weakening the quality of timber. Some scholars believe that Darwin was aware of Mr. Matthew's work prior to the publication of his first edition of Origin of Species (1861). Matthew's letter to Darwin stating his claim to natural selection was published in Gardeners' Chronicle: 7 April 1860. In his reply to Matthew ( Gardeners' Chronicle: 21 April 1860), Darwin apologized for his entire "ignorance" of Matthew's publication. In his third edition of the Origin of Species, Darwin cites Matthew's work under the section entitled "An Historical Sketch of the Recent Progress of Opinion of the Origin of Species."

      "In 1831 Mr. Patrick Matthew published his work on 'Naval Timber and Arboriculture,' in which he gives precisely the same view on the origin of species as that (presently to be alluded to) propounded by Mr. Wallace and myself on the 'Linnean Journal,' and as that enlarged in the present volume. Unfortunately the view was given by Mr. Matthew very briefly in scattered passages in an Appendix to a work on a different subject, so that it remained unnoticed until Mr. Matthew himself drew attention to it in the cellent history of opinion on this subject ... He clearly saw, however, the full force of the principle of natural selection. In answer to a letter of mine (published in Gard. Chron., April 13th), fully acknowledging that Mr. Matthew had anticipated me, he with generous candour wrote a letter (Gard. Chron. May 12th) containing the following passage:----"To me the conception of this law of Nature came intuitively as a self-evident fact, almost without an effort of concentrated thought. Mr. Darwin here seems to have more merit in the discovery than I have had; to me it did not appear a discovery. He seems to have worked it out by inductive reason, slowly and with due caution to have made his way synthetically from fact to fact onwards; while with me it was by a general glance at the scheme of Nature that I estimated this select production of species as an ŕ priori recognisable fact----an axiom requiring only to be pointed out to be admitted by unprejudiced minds of sufficient grasp."


    23. Symbiogenesis: Genomer Mergers

  110. Another scientific hypothesis known as symbiogenesis, is described in the book entitled Acquiring Genomes: A Theory of the Origins of Species by L. Margulis and D. Sagan (2002). According to the authors, genomic mergers are a major source of genetic variability leading to the evolution of species. Instead of relying on the hit-or-miss method of random mutations, symbiogenesis provides advantageous genetic combinations through the fusion of entire genomes from two or more organisms. This phenomenon may have been a major factor in the evolution of land plants from lichen-like ancestors. In 1981, Lynn Margulis also proposed the endosymbiont hypothesis to explain the origin of organelles within eukaryotic cells. According to endosymbiosis, cellular organelles (mitochondria and chloroplasts) originated from bacteria and cyanobacteria that became incorporated within living cells. When these original hypotheses have been repeatedly tested and scrutinized by different scientists, they may become scientific theories.

  111. The arise of photosynthetic organelles called chloroplasts represented a major step in the evolution and diversification of plant life on earth. This event had a significant effect on the evolution of animal life that depended on the plants for food, either directly in the case of herbivores, or indirectly in the case of carnivores. Chloroplasts exhibit remarkable similarities with cells of cyanobacteria, and may have shared a common prokaryotic ancestry. Indeed, the outer membrane structure and circular DNA molecules of chloroplasts and mitochondria are very similar to individual prokaroytic cells. According to the endosymbiont hypothesis (or endosymbiont theory for those who are less skeptical), ancient photosynthetic prokaryotic cells became incorporated within the cells of algae or ancestral plants, forming stable mutualistic symbionts known as chloroplasts. Mitochondria may have had a similar origin. Without chloroplasts and oxygen-producing photosynthesis, the amazing diversity of today's plants and animals may have never evolved.

  112. According to Margulis and Sagan (2002), there is even a green photosynthetic animal named Elysia viridis, a minute slug (saccoglossan opisthobranch) that never feeds throughout its adult life. Instead, it obtains carbohydrate-rich molecules by bathing in the sunlight. This slug evolved from algae-eating ancestors, only the algal cells entered the slug's tissue and remained their as photobionts (photosynthetic symbionts). According to some invertebrate zoology textbooks, the chloroplasts from algae cells are sucked into the slug's gut and incorporated within digestive gland cells where photosynthesis occurs.

  113. There are numerous examples of plants and animals that contain microbial symbionts within their tissues, including bacteria, cyanobacteria, protozoans and algal cells. Cycads, water ferns (Azolla), legumes and the tropical flowering plant Gunnera contain nitrogen-fixing bacteria in their tissues; sea anemones and corals contain photosynthetic unicellular algae (zooanthellae and zoochlorellae); the rumen of cattle contain cellulose-digesting bacteria; termite guts contain flagellated protists which contain wood-digesting bacteria; and human intestines contain bacteria that produce essential B vitamins.

    The water fern Azolla filiculoides contains colonies of filamentous cyanobacteria (Anabaena azollae) within cavities in its leaves. [See magnified inset.] These two organisms once formed an intimate symbiotic marriage many millions of years ago and have remained together ever since. Azolla provides a protected place for the Anabaena to survive at the surface of ponds and streams in full sunlight. Like other nitrogen-fixing organisms, colonies of Anabaena convert inert atmospheric nitrogen into ammonia, a form of nitrogen that is available to Azolla and other plants. Nitrogen-fixation occurs in oval cells called heterocysts (red arrow).

  114. Lichens are one of the best examples of symbiogenesis involving the fusion of algal and fungal genomes (kingdoms Protista and Fungi). Some lichens include the genome of a third kingdom Monera because they contain prokaryotic cells of cyanobacteria. In the case of lichens, this genomic merger has enabled these organisms to survive in some of the most inhospitable environments on earth, where neither symbiont could survive on its own. In fact, lichens are an excellent example of synergism because the whole is truly greater than the sum of its parts. The algal (photobiont) and fungal (mycobiont) components develop into a unique body form with morphological features quite different from either symbiont.

    Center: British soldiers (Cladonia cristatella), a soil lichen with upright stalks (podetia) bearing bright red spore-bearing apothecia at the tips. At the bottom of the centrifuge tube (A), the fungal component of this lichen (also named C. cristatella) has grown into a white, amorphous blob without its algal symbiont. In the right test tube (B), the algal symbiont (Trebouxia erici) has grown into a mass of bright green cells. Only when the genomes of the two symbionts form the "marriage" known as lichen is the unique structure of "British soldiers" formed. In true synergistic fashion, this lichen is truly more than the sum of its parts. For example, the podetium is a unique lichen structure that is not produced by the algal or fungal components.

    Some Other Examples Of Synergism In Lichens: Lichens Produce Structures
    That Are Not Found In Either Of Its Fungal or Photosynthetic Algal Symbionts

    Podetia are asexual reproductive structures produced by lichens, but not the algal or fungal symbionts. The podetium bears microscopic granules called soredia. Each soredium contains fungal hyphae wrapped around algal cells. The soredia become airborne and carry the lichen symbionts to different locations where a new colony can grow. This mechanism appears to be more efficient than starting a new lichen by the chance encounter of algal cells and fungal spores.

    Soralia are small breaks (pustules) in the lichen thallus where masses of soredia erupt. The microscopic soredia become airborne and travel to new locations. Isidea are pimple-like protuberances from the lichen thallus containing fungal hyphae and algal cells. They readily become detached and develop into new colonies. Soralia, soredia, podetia and isidia are unique lichen characteristics.

    Lichen Crust On Rocks & Boulders
    Marriage Between Azolla & Anabaena
      Prokaryotic Cells & Nitrogen Fixation  

  115. Both Darwin and Wallace are credited with the scientific hypothesis of evolution by means of natural selection. This hypothesis has been tested repeatedly by scientists during the past century and it is now elevated to the status of a scientific theory. Our knowledge of the evolution of life on this planet has grown considerably during the past 147 years since the time of Darwin. In fact, the term "Darwinist" repeatedly used in the intelligent design textbook Of Pandas and People is misleading. Does Darwinist refer to one who believes in the teachings of Darwin, or one that follows the modern scientific theory of evolution that encompasses many new concepts since the time of Darwin? The latter interpretation of evolution includes substantial information from the fields of genetics and molecular biology and is often referred to as neoDarwinism.


    24. Coevolution Between The Fig & Its Wasp
    A Complex and Remarkable Life Cycle That Defies Oversimplifications and Generalizations

  116. One of the most remarkable examples of coevolution between a plant and an insect is the fig tree and its symbiotic wasp. Minute male and female fig wasps are borne inside hollow, fleshy, flower-bearing structures called syconia. [The syconium is what most people associate with the tasty fruit of a fig, but technically it is not a true fruit.] The syconium is lined on the inside with hundreds of tiny, apetalous, pollen-bearing male flowers, long-style, seed-bearing female flowers, and short-style female flowers. Fig wasps develop from eggs laid inside the ovaries of the short-style female flowers (one egg per flower). In about half of the fig species (referred to as monoecious), male flowers and the long and short-style female flowers occur in the same bisexual syconium; but in all other fig species (referred to as dioecious or gynodioecious), the seed-producing, long-style female flowers only occur in unisexual syconia on female trees, while pollen-bearing male flowers and wasp-bearing, short-style female flowers occur in the same syconia on male trees. In the common edible fig (Ficus carica) the male trees are called caprifigs. [The prefix capri refers to goat, and these figs were apparently fed to goats.] Wasp eggs are not laid in the ovaries of long-style flowers because the wasp's ovipositor cannot reach the ovary; therefore, the ovary develops a seed rather than a wasp (assuming it is pollinated). Without the pollinator wasps transferring pollen from one syconium to another, the female flowers inside would not get pollinated and no seeds would be produced (a catastrophe for the fig tree). This remarkable floral dimorphism (heterostyly) is how the fig tree produces seeds (on female trees) while still maintaining its vital, "in-house" population of symbiotic wasps on male trees. There are approximately 830 species of figs (genus Ficus), mostly distributed throughout tropical regions of the world. They all have one or more pollinator wasps in the family Agaonidae that enter their syconia through a small opening (called an ostiole) to pollinate the female flowers inside. Although pollinator wasps are often host specific, one pollinator can have more than one host (J.M. Cook and J.-Y. Rasplus, 2003). In addition, the syconium may contain one or more non-pollinating wasps in different wasp families. Like the symbiotic pollinator wasps, the nonpollinators have flattened heads and bodies, and are perfectly adapted to squeeze between the ostiolar bracts of receptive syconia. This is yet another example of convergent evolution. Depending on the fig species, pollen is transferred to the female flowers, either passively or purposively. In the latter case the wasp actually transfers pollen from pollen baskets (corbiculae) on the underside of her thorax to the stigma.

    Life cycle of the common fig (Ficus carica). Style length is genetically determined and it is vital that syconia on seed-bearing female trees have styles longer than the female wasp's ovipositor. Unable to reach the ovaries of these flowers, she does not lay eggs (oviposit). Therefore, a seed develops inside the ovary rather than a wasp larva. She can only oviposit in the short-style female flowers on "male" trees called caprifigs. Caprifig trees produce pollen and the crucial pollinator wasps (Blastophaga psenes). In some common figs termed "caducous" or early deciduous, the immature female syconium drops from the tree if the flowers inside are not pollinated. There are many cultivated "parthenocarpic" varities of the common fig in which the syconia develop on female trees wthout wasp pollination (caprification). The ripe syconia are fleshy and edible; however, the numerous ovaries (drupelets) inside are hollow and seedless.

  117. In short-style female flowers, the wasp inserts her ovipositor down the stylar canal and lays an egg in the ovary of the flower. The subsequent larva feeds on endosperm tissue initiated by the ovipositing pollinator wasp. Since the endosperm in some figs may be initiated parthenogenetically (without pollination and fertilization), possibly by a mechanical or chemical stimulus during oviposition, food tissue for the developing larva functions like a minute gall. Style length is genetically controlled, and it is important for the tree to have style lengths longer than the wasp's ovipositor in long-style flowers so that seeds can develop in these ovaries. It is also important to have flowers with short styles so that female wasps can lay eggs (oviposit) in the ovaries. "Bogus" fig wasps (parasitoids and inquilines) with extra long ovipositors present a formidable problem to figs. They can readily lay eggs in long-style flowers, and can even penetrate the syconium wall without pollinating the female flowers inside. Some dioecious figs can counter this problem by simply aborting unpollinated syconia, thus ridding itself of seedless syconia. This strategy does not work on monoecious figs with multiple style lengths in the same syconium. Dioecious figs may represent an advanced (further evolved) species.


    Overwintering mame crop of syconia.

    A fig wasp larva inside the ovary of a short-style female flower in an overwintering mamme syconium. This is the leafless dormant season for the caprifig (Ficus carica). Since the previous mammoni crop of syconia do not produce pollen, the larva fed on parthenogenetic endosperm tissue that developed without pollination. The initiation of endosperm tissue after oviposition by the female wasp meets the criterion for gall formation. The larva consumes the galled tissue within the ovary wall. After metamorphosis, the adult male wasp chews a hole through the ovary wall and exits the female flower. He crawls to another short-style female flower that contains a mature female wasp. He climbs up on the ovary of the flower, bites a fertilization hole in the ovary wall, and inserts his long, slender abdomen into the opening, thus inseminating the female. After being inseminated, the female crawls out of the fertilization hole through the ovary wall initially made by the male. Wasp larva photographed in January 2009.

        Coevolution Of A Fig & Its Symbiotic Wasp    
    The Calimyrna Fig & Its Pollinator Wasp
    The Remarkable Fig/Fig Wasp Scenario
    Sex Determination Of The Common Fig
    Articles About Figs On Wayne's Word
    Do Fig Wasps Really Produce A Gall?

  118. It should be noted here that some fig species have two or more species of symbiotic wasp pollinators. In fact, the classic one-fig/one-wasp partnership has been challenged by D. Molbo, et al. (Proceedings of the National Academy of Sciences 100, 2003). S. G. Compton, et al. (African Entomology, 2009) found three or more species of pollinator agaonid wasps in the syconia of Ficus natalensis. Fig wasp species may be closely related sister taxa, or may be quite different from each other. This indicates both long-term coexistence on shared hosts and relatively recent colonization of fig species. Fig syconia may also contain wasps who do not pollinate the female flowers inside. It is clear that the fig/fig wasp scenario is far more complicated than originally described. In fact, Richard Dawkins (personal communication, 1996) agrees that it is a difficult subject to adequately cover in laymen publications about evolution. There are literally thousands of articles on this subject with numerous exceptions and contradictions to any universal fig wasp life cycle pattern.

    A. Close-up view of a male and female fig wasp (Pleistodontes imperialis) that inhabits the syconia of the Australian rustyleaf fig (Ficus rubiginosa). The slender ovipositor on female wasp is too short to penetrate the ovary of long-style flowers; therefore she does not lay eggs in these flowers. The smaller, wingless male has large mandibles and a greatly reduced body which has two primary purposes: (1) Inseminating the female and (2) Chewing exit tunnels through the syconium wall through which the females escape. The "eye" of an ordinary sewing needle is shown for a size comparison.

    B. A non-pollinator "bogus" fig wasp collected from the syconium of the Baja California wild fig (Ficus palmeri or possibly Ficus brandegeei). The ovipositor is much longer than the symbiotic pollinator wasp. In fact, some non-pollinator wasps can penetrate the entire syconium wall from the outside. They can also lay eggs in long-style fig flowers reserved for fig seeds. Consequently, no seeds are produced in these flowers. In addition, these "bogus" fig wasps do not pollinate fig flowers. Although they do not benefit the fig tree, non-pollinator wasps of the families Torymidae and Eurytomidae are common inhabitants of New World monoecious fig syconia. Their coexistence with natural fig pollinator wasps is a complex and perplexing coevolutionary problem in fig biology.

     Size Of Sewing Needle In Wayne's Word Images 
    Ficus palmeri In Mtns & Coastal Baja California

  119. According to Carole Kerdelhue and Jean-Yves Rasplus (Oikos Vol. 77, 1996), dioecious figs may have evolved from monoecious ancestral fig species due to selection pressure by non-pollinating fig wasps. Although these non-pollinator wasps belong to the same order Chalcidoidea as pollinators, many of them belong to different families. They do not benefit the fig and may even be harmful, especially when they compete with and/or parasitize the beneficial pollinator wasps. The non-pollinator, parasitic wasps never occur in the long-style flowers of syconia on female trees, and non-pollinator wasps are uncommon in the syconia of male trees. Therefore, seed production in syconia on female trees and pollinator wasp production in syconia on male trees are not diminished, as in the syconia of monoecious figs containing detrimental non-pollinator wasps. Kerdelhue and Rasplus, 1996) state that no gall-makers that lay eggs through the syconium wall (after pollination by beneficial pollinator wasps) have ever been found so far in dioecious figs; however, agaonid wasps of the genus Philotrypesis that oviposit through the syconium wall are well known in the dioecious edible fig (Ficus carica). In general, having separate male and female trees in the population may be an adaptive advantage with regards to pollination and seed production.

    Left: A dioecious fig showing short-style and long-style female flowers inside syconia of male and female trees. Non-pollinator wasps typically do not inhabit these syconia.

    Right: The monoecious syconium of the South African Ficus sur contains long-style and short-style female flowers densely packed together in a layer that lines the inner cavity of the syconium. Although the styles all form a relatively continuous stigmatic layer called a synstigma (i.e. all stigmas in the same plane) within the syconium, the ovaries may be deep or shallow relative to the synstigma depending on the length of their flower stalks (pedicels). There are four style lengths (heterostyly) and four ovary positions designated by different colored ovaries. Generally, the deep-seated black ovaries (on short pedicels) with long styles each contain a seed, while the shallow yellow ovaries (on long pedicels) with short styles each contain a wasp larva. A pollinator wasp walking on this "bed" of styles (synstigma) can insert her ovipositor down the short style and easily penetrate the ovary where she lays an egg. The deep-seated, long-style ovaries are out of reach for her ovipositor (style longer than her ovipositor), and consequently these ovaries develop seeds rather than wasp larvae. If the non-pollinating wasps are very numerous, the medium layers 1 and 2 (yellow and green ovaries) will be occupied entirely by exploiters and these occupied flowers will not produce seeds or pollinator wasps. According to Kerdelhue and Rasplus (1996), this probably represents a high cost to the fig with regard to seed production.

    The above syconium structure is not the case for all monoecious figs. According to Zhang, et al. (Annals of the Entomological Society of America Vol. 102, 2009), the Asian fig F. curtipes and relatives (subgenus Urostigma, subsection Conosycea) lack a synstigma, which is replaced by an irregular mass of elongate stigmas. The stigmas are unbranched, slightly curved, and only slightly broader than the style. Instead of walking on a mat of stigma tips (synstigma), the female wasps frequently stumble and fall between different stigmas as they attempt to find oviposition sites. The lack of a fused synstigma enables the wasps to insert their ovipositors at the basal end of the stigmas, not at the top of stigma as described in other species, which reduces the length of ovipositor that has to be inserted. Thus, the ovipositor of the pollinator Eupristina sp. is sufficiently long enough to reach all the ovules. In other figs with unbranched stigmas (subgenus Sycomorus) and figs with branched stigmas (subgenera Urostigma and Pharmacoscea), oviposition occurs at the top of stigma. Oviposition behavior in fig wasps is therefore not universal, and is responsive to variation in floral structure within their host figs. There may indeed be factors other than style length preventing oviposition in long-style flowers.


    25. Vicarious Selection In Dioecious Figs
    A plausible explanation why pollinator wasps don't evolve longer ovipositors so they can oviposit in the ovaries of long-style female flowers. Male and female syconia are virtually indistinguishable in external appearance. Selection takes place in male syconia of caprifig.

  120. In his book "Climbing Mount Improbable (1996), Richard Dawkins devotes Chapter 10 to the fig/fig wasp coevolution and the model for vicarious selection proposed by Grafen and Godfray (Proceedings of the Royal Society, 1991). In vicarious selection of the dioecious fig subgenus Urostigma, morphology (style and ovipositor length), and wasp behavior (purposive loading and unloading of pollen) is taking place in wasps who enter and leave male syconia containing short-style female flowers on male trees. This selection is crucial for the perpetuation of fig trees when wasps enter female syconia on female trees (which superficially resemble male syconia). Female syconia produce seeds (the vital genetic link for fig trees) and are a genetic graveyard for wasps because they cannot oviposit in the long-style female flowers. The female wasps die in these syconia. For wasps in female syconia, mutations for a longer ovipositor that could reach the ovary of long-style flowers would not be passed on. For wasps in male syconia, there is no selective advantage for longer ovipositors because they are perfectly adapted for laying eggs in the ovaries of short-style flowers. Vicarious selection does not explain the evolution of ovipositor length in all figs, particularly the numerouas monoecious species. The fig/fig wasp scenario is much more complicated, with many variations in the life cycles depending on the different subgenera. Unfortunately, it is beyond the scope of this discussion.

     Key To Subgroups Of Dioecious (Gynodioecious) Figs 


    26. Coevolution Between Swollen Thorn Acacia & Acacia Ant

  121. Another remarkable example of coevolution between a tree and an insect is the acacia and its symbiotic ant. Some species of Central American swollen-thorn acacias lack the chemical defenses of most other acacias to deal with their predators and competition. Without bitter alkaloids, ravaging insects and browsing mammals eat the leaves and branches, slowing the growth of the acacias and allowing fast-growing, competing vegetation to shade them out. Symbiotic stinging ants have taken over this vital defense role, protecting the acacia from hungry herbivores and pruning away competing plants. The ants live inside inflated thorns (stipular spines) at the base of the leaves. The ants will even clear away seedlings of fast-growing competing plants around the base of the acacia. The acacia tree provides housing for the ants in the form of hollowed-out thorns. It provides nourishment in the form of carbohydrate-rich nectar from glands on the leaf stalks (petioles). It also provides protein-lipid Beltian bodies from its leaflet tips. There is no other known function for these tiny, yellowish morsels other than to provide food for its ants. Swollen thorn acacias of lowland Central America include Acacia cornigera, A. collinsii, A. hindsii, A. sphaerocephala, and A. cookii. The ant colonies inhabiting these trees typically belong to the genus Pseudomyrmex.

    Three species of Acacia with swollen stipular spines that are hollowed out and occupied by symbiotic ants. Left: The bullhorn acacia (Acacia cornigera), a swollen-thorn acacia native to Mexico and Central America. In its native habitat, colonies of stinging ants (Pseudomyrmex ferruginea) occupy the hollowed-out thorns and fiercely defend the tree against ravaging insects, browsing mammals and epiphytic vines. In return, the host supplies its little guardian ants with protein-lipid Beltian bodies from its leaflet tips (yellowish granules in photo) and carbohydrate-rich nectar from a gland on its petiole just above the pair of spines (white arrow). Center: Another Central American swollen thorn acacia (A. collinsii) with an acacia ant (P. ferruginea) sipping nectar from the petiolar nectary. Right: The African whistling thorn acacia (A. drepanolobium). The common name comes from the whistling sound that is produced when wind blows across the large hollowed-out thorns. Since the "thorns" on these trees are technically pairs of modified stipules, they are more correctly referred to as stipular spines. In order to have consistent monophyleic cladograms based on chloroplast DNA, these three Acacia species of have been moved to the genus Vachellia (See section 12).

  122. Nests of at least a dozen bird species have been reported in swollen thorn acacia trees that contain Pseudomyrmex ants (Janzen, 1969). The relationship between birds nesting in acacias inhabited by ants appears to be commensal, because ants that protect acacias against herbivores also offer protection against avian nest predators (Janzen, 1969, 1983). On the other hand, the birds do not seem to provide any benefit to the acacias or ants. A symbiotic relationship in which one organism is benefited while the other is neither benefited nor harmed is called commensalism. Unlike the relationship between the fig and fig wasp, the acacia and acacia ant is probably not a good example of mutualism. Daniel Janzen also reported predation on the ants by certain birds, primarily by splitting open the thorns to access larvae and workers. In the latter case, the relationship between the acacia ant and bird could be considered parasitism (at least in part), since one member is actually harmed by the relationship.

    See The Wayne's Word Article About Acacias
    See Stipular Spines Of Swollen-Thorn Acacias
    Necklace & Seed Doll Made Of Acacia Spines

    Whistling Thorn Symbiosis May Be One-Sided:

    Additional complexities about Africa's whistling thorn (Acacia drepanolobium) are discussed in a recent article by Maureen Stanton and Truman Young in Natural History Volume 108 (November 1999). Studies by Stanton and Young reveal that four species of stinging ants live symbiotically on A. drepanolobium: Crematogaster mimosae, C. nigriceps, C. sjostedti, and Tetraponera penzigi. Their studies also reveal that the symbiotic relationship between some of these ant species and their host acacia may not be equally beneficial to both partners. Since these different species of ants are rival enemies, they occupy separate trees. If acacia branches containing rival ant colonies make contact, the different species of ants will fight each other, with the loser being evicted from its tree. Unlike the Central American thorn acacias that provide their ant warriors with protein-lipid Beltian bodies on leaflet tips, the whistling thorn provides no such service. This forces the ants to leave the tree to forage for insects and other protein-rich foods which they bring back to the developing ant larvae living inside the swollen thorns. According to Stanton and Young, refuse pushed out of the thorn nests may help to fertilize the tree.

    The relationship between some of these ant species and their acacia is not completely mutualistic because it may harm the acacia tree. Crematogaster mimosae and C. sjostedti both tend scale insects that feed on the tree's vascular system, milking the aphid-like insects for their nutritive honeydew secretions. In fact, C. sjostedti pays little attention to herbivores that attempt to feed on the tree. The latter species also nests in hollow spaces within dead and dying branches, rather than in the swollen thorns. Colonies even thrive in the stumps of dead trees. To make matters worse, this species of ant often comes out the winner in battles with other ant species over the possession of a tree. According to Stanton and Young, the balance in a once mutualistic relationship has shifted in favor of one partner (the ant) at the expense of the other (the tree).

    Although not as extreme as Crematogaster sjostedti, the relationship between C. nigriceps and its acacia host is also one-sided in favor of the ant. This ant species chews off the tips of growing shoots, including leaf and flower buds, thus pruning and sterilizing the tree. New branches are allowed to grow mainly in the proximity of swollen thorns, thus ensuring nectar-rich petiolar nectaries (glands) on new leaves easily accessible to worker ants inside the thorns. Over time, this pruning by ants changes the growth rate and shape of the tree canopy, compared with trees occupied by other ant species. In addition, pruning is more radical on sides adjacent to rival ant trees, thus reducing the chance of contact with branches of rival trees containing more aggressive ant species.


    27. Hybridization Between 2 Species Of Desert Harvester Ants

    Harvester Ant Workers: Hybrids Between Pogonomyrmex rugosus & P. barbatus:
    Another Truly Remarkable Example Of Genetic Diversity, Selection & Coevolution

    Sex determination in the more than 12,000 species of ants is typical of the enormous insect order Hymenoptera, including bees and wasps. The method is called "haplodiploidy." Males develop from unfertilized eggs and are haploid with one set of maternal chromosomes. They are not identical clones of their queen mother because of crossing over and random assortment of chromosomes during meiosis (oogenesis). Deleterious (unfavorable) recessive genes are quickly weeded out in haploid males because they are expressed and cannont be masked by dominant genes. Females develop from fertilized eggs and are diploid with two sets of chromosomes. Some references say that larvae destined to become sexually mature queens are "well-nurtured," presumably similar to royal jelly in honey bees; however, other reputable authoritees state that selection of a queen in some ant species is a lot more complicated and may involve special eggs destined to become queens (see next paragraph).

    In zones of hybridization, Pogonomyrmex harvester ant workers of the southwestern U.S. are hybrids between P. rugosus and P. barbatus. They possess the best genetic traits of two species. The queen of each species mates with the males of opposite species. Sexually mature ants (queens and winged males) are purebreds: They are offspring of queen and males of the same species. Young queens need to mate with their own species to produce more purebred queens. They need to mate with the other species to produce "superorganism" workers. This strategy appears to be evolutionarily advantageous to both species. For more information, please refer to articles in bibliography by S.H, Cahan, L. Keller and T. Schwander (2003-2007).

    Dark harvester ants (Pogonomyrmex rugosus) or possibly hybrids with P. barbatus.

    Comparison Of Pogonomyrmex Hybrid Workers With A Mule

    If the workers of an ant nest can be thought of as the superorganism's body, and the sexuals (queens & males) can be thought of as the superorganism's genetic material, it is as though an animal with the body of a mule has the genetic make-up of a horse and donkey!

    Although Pogonomyrmex hybrid workers form a colony and the mule is a single organism, they make an interesting comparison. They both involve a cross between two species that forms a stronger hybrid offspring with the best traits of its parents. The ant colony of hybrid workers functions as a unit that could be described as a "superorganism." This is similar to the "Borg Collective" in Star Strek: The Next Generation.

    The female horse (mare) mates with a male horse (stallion) to produce more male and female horses. If she mates with a male donkey (jackass) she can produce a male or female mule. The mule is a sterile hybrid with the body size of a horse and the sure-footedness and endurance of a donkey. That is why the mule is essentially a "superorganism" used as a powerful pack animal. In the case of Pogonomyrmex, the hybrid "super-ants" are the workers. An original 20 mule team wagon train was used in 1885 to haul borax from Death Valley to Mojave, a distance of 165 miles. The borax weighed 24 tons and the entire wagon train weighed 36.5 tons (gross weight). The last wagon carried water for the mules during the hot, 10 day journey across the Mojave Desert. Today, a load of this size would be pulled by a 600 horse power Kenworth T-2000 tractor with an air conditioned cab!

      More Information About The Mule On Wayne's Word  
    See The Wayne's Word Page On Subfamilies Of Ants

    In a previous paragraph I compared ants with the "Borg" of Star Trek, a fictional cybernetic race controlled by drones. This is probably not an accurate comparison because the Borg apparently have centralized control by the "Borg Queen." Ant colonies exhibit "swarm intelligence" with the collective behavior of a decentralized system. The individual units (workers & soldiers) are sterile females that operate without a power hierarchy or permanent leader. The queen's role is basically an egg machine to reproduce and perpetuate the colony. The individual worker ants are like cells of an organism, and they are able to communicate with each other by the release of pheromones. This social unity is evident in extreme warfare between different colonies, and explains how colonies recognize "self" from "alien" ants. Recognition between cells of an organism is also controlled by chemicals.

    One of the worst ecological disasters in southern California is the introduction of the Argentine ant (Linepithema humile). They are a serious pest that tends aphids and scale insects, kills off the native harvester ants that our coast horned lizard depends upon, and destroys baby birds in their nest. On a recent trip to Maui I discovered that Argentine ants in Haleakala National Park are threatening the native pollinators of the endemic, rare and endangered silver sword (Argyroxiphium sandwicense ssp. macrocephalum). Many of our native ant species have been completely eliminated from urbanized areas of southern California by the Argentine ant. This is particularly true in areas that are regularly watered, providing damp, cool habitats for Linepithema. Although these ants are only 3 mm long, they are very aggressive and quickly annihilate other ant species, even larger ants with powerful jaws and stings. They overpower other species by their sheer numbers. Argentine ants in the U.S. are descendants of original colonizers that entered Louisiana in the late 1890's, as coffee ships from Brazil unloaded their cargo in New Orleans. U.S. populations are so closely related that different colonies with multiple queens can literally merge together into supercolonies. According to Mark Moffett (2011), the biggest of these supercolonies ranges from San Francisco to the Mexican border and may contain a trillion individuals!


    Winter Ant
    (Prenolepis imparis)
    Just when I thought there was no hope of survival for native California ants within the range of the Argentine ant supercolony, I came across a little native called the winter ant (Prenolepis imparis). Workers of this species may be able to survive the attacks of Argentine ants. I first noticed these shiny black ants in December 2012 near Palomar College, hence the common name of "winter ant." According to Trevor R. Sorrells, et al., Department of Biology, Stanford University (2011), winter ants secrete a hydrocarbon mixture that is lethal to Argentine ants, thus providing an effective defense against this invasive species from South America. Please refer to following link in the peer-reviewed journal PLOS ONE Volume 6 (4) 2011.


    28. Natural Selection & Survival of the Fittest

  123. There are many remarkable examples of natural selection in animals where a particular adaptation has survival value. Some of these include camouflage (protective form & coloration), warning coloration and mimicry. The main evolutionary advantage for these adaptations is to avoid being eaten by predators long enough to pass on your genes to future generations, thus perpetuating the species. Consider Batesian mimicry in a harmless little snake with a banding pattern similar to a deadly Arizona coral snake (Micruroides euryxanthus). A predator might not attack this snake because of its coloration. Similar banding patterns among different species of poisonous coral snakes is termed Mullerian mimicry.

    Only one of these snakes has the banding pattern of a deadly Arizona coral snake (Micruroides euryxanthus). Helpful rhyme: "Red bordered by yellow, kills a fellow." If you guessed correctly on the banding pattern of the poisonous species, please do not feel overconfident in identifying all coral snakes and their mimics. The classic rhyme does not apply to the poisonous coral snake (Micrurus frontalis) native to Brazil.

    A striking South American lanternfly (Phosphora lanternaria). The enlarged head extension mimics the head of a small alligator. Some authorities have suggested that the reptilian head may ward off an attack by potential predators of this harmless, plant-eating insect. It has also been suggested that the head resembles an unshelled peanut; however, it is doubtful that any adaptive advantage can be gained by mimicking a peanut. These mimics are the derivation of the common names "gator" lanternfly and "peanut" lanternfly.

    Left: A Japanese giant hornet (Vespa mandarinia japonica). With their powerful mandibles, several dozen of these giant hornets can annihilate 30,000 European honey bees (Apis mellifera) in a few hours by quickly decapitating them. The hornets feed on the honey bee larvae. European honey bee stings do not phase the giant hornets and they simply have not evolved any defense against this large predator. The native Japanese honey bee (Apis cerana japonica) has evolved a clever strategy for killing this predator if it invades their nest. The bees do not attack the scout hornet, but instead allow it to enter their hive. Then a mob of several hundred worker bees envelop the invader and vibrate their flight muscles, thus raising the hornet's body temperature by 2 degrees Celsius. The large hornet body is vulnerable to an increase in temperature and 2 degrees is lethal. See the following two YouTube videos:

     Giant Hornets Attacking Nest Of European Honey Bees 
    Giant Hornet Invading Nest Of Japanese Honey Bee 

    Leafy sea dragon (Phycodurus eques), one of the most remarkable examples of camouflage in the animal kingdom. Native to southern Australia, this fish is difficult to distinguish from leafy seaweeds. In fact, at first glance it is hard to tell that it is a fish. Sea dragons belong to the order Solenichthyes, along with sea horses and pipefish.

    Additional Sea Dragon Images
    Plant & Animal Adaptation Links
     Plant & Animal Adaptation Images 


    29. Selection In Tardigrades: Are They Over-equipped?

    Tardigrades belong to a remarkable phylum of minute multicellular animals.

    They are adapted to extreme conditions, some of which are more severe than any earth environment. Does their origin defy natural selection?

  124. Tardigrades are microscopic, water-dwelling, segmented animals with eight legs. Depending on the species, they range in size from 0.1 to 1.5 mm long. They are called "water bears," in reference to their stumpy legs tipped with claws, and especially their lumbering gait. More than 1,000 species have been described. They occur throughout the world in some of the most inhospitable places, from high peaks in the Himalayas (above 20,000 ft) to boiling water near heat vents on the ocean floor, and from the Arctic tundra to vast ice fields of Antarctica. During severe environmental conditions that would kill most creatures on earth, tardigrades roll up into little dehydrated balls called "tuns" where they survive for extended periods of time. This dormancy phenomenon is called cryptobiosis (or anabiosis). Their ability to survive in this desiccated state for long periods is largely dependent on high levels of the non-reducing sugar trehalose that protects their tissues and preserves the integrity of intracellular organelles, membranes and DNA. Tardigrade physiology has led to the discovery of "dry vaccines" that don't require refrigeration and thus can be delivered and stored at room temperature. Some species can survive temperatures near absolute zero (-273° C) where liquids and gasses freeze solid; some can survive temperatures up to 151° C (304° F); some can live without water for 10 years; some can survive 1,000 times more gamma radiation than other animals (tardigrades can withstand 570,000 rads of X-ray radiation while 500 rads would kill a human); some can withstand pressures up to 6,000 atmospheres (more than the deepest ocean trench), and some can actually live for a while in a vacuum. In fact, tardigrades were taken into earth orbit on the Russian robotic spacecraft FOTON-M3 and survived 10 days in space. Upon returning to earth and hydrated, many actually laid eggs that hatched normally!

    Lateral (side) view of the exoskeleton of an aquatic tardigrade (Hypsibius sp.) containing 5 eggs. There are 4 pairs of stout, stumpy legs, each tipped with several slender claws. The name "water bear" refers to its deliberate "pawing" sort of locomotion. Thomas Huxley, English naturalist and good friend of Charles Darwin, gave tardigrades this name in 1869. Photographed with a Sony W-300 digital camera through an Olympus laboratory grade compound microscope (400x magnification).

    Trehalose is a disaccharide sugar formed from two glucose units joined by a 1-1 alpha bond. The bonding makes trehalose very stable even under extreme conditions of temperature, pressure, dehydration and pH (acidity). Since it is a nonreducing, it doesn't react with amino acids or proteins. During long periods of desiccation, trehalose maintains the integrity of intracellular organelles, including mitochondria and plasma membranes. Rehydration then allows normal cellular activity to be resumed without the lethal damage that normally follows the dehydration/rehydration cycle.

  125. Trehalose: The Remarkable Sugar Of Tardigrades
  126. When tardigrades dry out, the glucose in their bodies changes into trehalose as they enter the dormant state of cryptobiosis. It apparently forms a "gel phase" when cells dehydrate, thus maintaining the integrity of intracellular organelles (e.g. mitochondria and membranes) by splinting them in position. The resurrection plant (Selaginella) also contains trehalose. This remarkable plant of arid desert regions becomes cracked and desiccated, but rapidly revives and turns green after a rain. Trehalose also explains how certain crustose rock lichens can survive for months without water and then quickly revive and become metabolically active when they receive water.

     See Desiccated & Rehydrated Resurrection Plant 

    There are currently three main hypotheses to explain the mechanisms by which trehalose sugars stabilize living systems during extreme cycles of freeze-thaw, heat-cooling and dehydration-rehydration (Pereira, et al. 2004). The Water-Replacement Hypothesis suggests that during drying, sugars can substitute for water molecules (by forming hydrogen bonds) around the polar and charged groups present in phospholipid membranes and proteins, thereby stabilizing their native structure in the absence of water and preventing ice formation. The Water Entrapment Hypothesis, in contrast, proposes that sugars concentrate residual water molecules close to the biostructure, thereby preserving its solvation and native properties. The Vitrification Hypothesis suggests that trehalose sugars are good vitrifying agents and protect biostructures through the formation of amorphous glasses (non-crystalline solids), thereby preventing denaturation or mechanical damage to cells and tissues.

    The enzyme trehalase breaks trehalose into two glucose molecules. This is the primary glucose source in insects for the rapid energy requirements of flight. Humans also posses the enzyme trehalase, although it is not abundant in most people. Several on-line sites suggest that replacement of dietary sucrose with trehalose may help to reduce the accumulation of malformed, clumping proteins in the brain and spinal cord associated with neurodegenerative diseases, such as Alzheimer's, Parkinson's and Huntington's. In addition, trehalose has a low glycemic index and reportedly does not spike the glucose level in diabetics. I have not verified all these medical claims in reputable medical journals. Could this be a sweetener that is actually good for you?

  127. Advocates of intelligent design believe that tardigrades defy evolution by natural selection because they are adapted to extreme conditions, some of which are more severe than any earth environment. Creationists maintain that natural selection can only select characteristics necessary for immediate survival. Consequently, evolution cannot be expected to "over-equip" species for a host of environments that they have never faced. Advocates of the panspermia hypothesis believe that tardigrades had an extraterrestrial origin, although DNA sequencing data indicate that the phylum Tardigrada (tardigrades) is a sister clade with the phylum Arthropoda (arthropods), and both phyla (Tardigrada + Arthropoda) form a sister clade with the phylum Onychophora (velvet worms).

  128. A strong case to support the evolution of "over-equipped" species is "gene duplication" in diploid organisms that greatly increases genetic variability. One of the truly remarkable examples of gene duplication is the antibody mediated immune system of animals. Gene duplication is a plausible explanation for how organisms can produce antibodies against different antigens, even synthetic antigen proteins that animals have never been exposed to. Using this model, animals would not need separate genes for every antigen they will ever encounter. This mechanism goes way beyond the simple evolution of adaptations based on Darwin's theory of evolution by means of natural selection.

      See Section 5: Mechanism For Immune Antibody Production  

    An aquatic tardigrade of the genus Hypsibius. Its length is approximately 184 micrometers (microns), about the same length as the hair follicle mite Demodex brevis. It is much smaller than a grain of common table salt (NaCl). The image was enhanced with Photoshop to bring out detail of the claws. Magnification 400x.

    See Demodex On The Table Of Cell Sizes  
      See Tardigrade Discovered On Owen's Peak  

    Tardigrade (Hypsibius):  10 MB .MPG File
    Tardigrade (Hypsibius):  5 MB .M4V file


    30. Faith & The Existence Of Coconut Pearls

  129. An example of a common theory based on faith is the existence of coconut pearls, beautiful calcareous stones that allegedly form inside coconuts. Most records of coconut pearls are second-hand accounts where the owner never actually saw the pearl within its original coconut. Published first-hand accounts have been shown to be fraudulent. All tested coconut pearls have been shown to be pearls and polished shells from giant clams (Tridacna) of Malaysia. They were carefully inserted into coconuts to fool the owners, or simply came with fictitious stories about their origin. In fact, I almost purchased one from Singapore until I discovered its price of $60,000 U.S. dollars! Although millions of coconuts are harvested annually, there is no documented coconut pearl that has survived scientific analysis by authorities. Without empirical evidence, the existence of coconut pearls appears to be a myth (Armstrong, 2005 & 2007). Completely independent of my research, Dr. J.V. Veldkamp of the National Herbarium of the Netherlands and editor of the prestigious journal Flora Malesiana Bulletin, has also been studying coconut pearls called "mestica calappa" and published a paper on this subject for Flora Malesiana Bulletin in 2002. Like myself, he is now convinced that they are a hoax and is updating his original article in a forthcoming issue of Flora Malesiana Bulletin.

  130. Some authors still maintain that coconut pearls exist and continue to perpetuate this assumption in the literature. They say: "Just because there is no proof of their existence, does this mean that coconut pearls do not exist?" A scientist would say: "With the complete lack of proof for the existence of coconut pearls, the probability of finding one inside a coconut is extremely unlikely, and their existence appears to be based on faith rather than objective facts." There are websites where you can actually purchase "coconut pearls." One site claims that the authenticity of their "coconut pearls" is based on psychic verification by a trained shaman. They also state that they cannot guarantee the authenticity of their "coconut pearls" with 100 percent certainty, but this "does not mean the pearls and stones are fake." I suppose it isn't too surprising to see "coconut pearls" for sale on the Internet since there are also websites offering extraterrestrial real estate for sale on the moon.

     See Disclaimer On The Existence Of Coconut Pearls 

    The "Maharajah coconut pearl." It was discovered on Celebes Island in the Java Sea and presented to Dr. David Fairchild in 1940. This alleged "pearl" given to Dr. Fairchild was not in its original coconut, so there is substantial doubt as to its authenticity.

     See Disclaimer On The Existence Of Coconut Pearls 


    31. Propositions For The Origin Of Life On Earth

  131. Religious debates over the origin of life are often false dichotomous arguments. If the scientific explanation is not adequate then the alternative argument for creation must be true. The problem here is that this debate is not limited to two alternative arguments. There are several scientific hypotheses for the origin of life and numerous explanations for supernatural creation throughout the world. In false dichotomous arguments, if one side is wrong this does not mean that the other side is correct. In true dichotomous arguments there are only two choices. If one side is false then the other side must be true. For example, in a dichotomous key to the duckweed family, one statement says that roots are present, while a second statement says that roots are absent. Only one of these statements is true regarding the duckweed species you are trying to identify.

    See A Simplified Dichotomous Key To The Duckweed Family
     See A Flow Chart Dichotomous Key To The Duckweed Family 

  132. There are literally thousands of non-scientific theories proposed for the origin of life, including intelligent design. Supernatural arguments for the origin of life are not scientific theories because they have no empirical evidence and cannot be tested or proven. They are based on faith in a creator (God). Advocates of intelligent design are very careful not to mention God as the designer. If the "designer" is not God, then is it an intelligent being from another galaxy? Advocates of intelligent design also argue that their "theory" has been tested and the results published in reputable, peer-reviewed scientific journals, but this is simply not the case. In 2004, an Intelligent Design article was accepted by the editor of Proceedings of the Biological Society of Washington without the approval of the Society's governing council. The 250 indignant members of this Society vehemently protested its publication. See "Creationism's Holy Grail: The Intelligent Design of a Peer-Reviewed Paper" by Robert Weitzel in (Skeptic Volume 11 (Number 4) 2005, pages 66-69. Although Charles Darwin mentioned a Creator in some editions of his Origin of Species, there is considerable speculation regarding his religious convictions. In a letter to Mr. J. Fordyce (1879) Darwin wrote: "... In my most extreme fluctuations I have never been an Atheist in the sense of denying the existence of God. I think that generally (and more and more as I grow older), but not always, that an Agnostic would be the most correct description of my state of mind." For more information about Darwin's religious beliefs, please refer to Finding Darwin's God by Kenneth R. Miller, HarperCollins, 1999.

  133. The following quotations come from the last two paragraphs of Chapter 24 in Darwin's Origin of Species (1859). They do not appear to be the words of an atheist:

      "Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created. To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual. When I view all beings not as special creations, but as the lineal descendents of some few beings which lived long before the first bed of the Silurian system was deposited, they seem to me to become ennobled. ..."

      ... There is grandeur in this view of life, with its several powers, having been originally breathed [by the Creator] into a few frms or into one; and that, whilst this planet has gone cycling on 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."

      "By the creator" was inserted into this last paragraph of Origin of Species in the 2nd edition (1860).

  134. As I stated above, Darwin expressed his agnostic state of mind in a letter to Mr. J. Fordyce in 1879 (K.R. Miller, 1999). However, in his autobiography he expressed a theistic point of view. In his old age Darwin wrote down his recollections for his own amusement and the interest of his children and their descendents. He completed the main narrative of 121 pages in 1876, but added 67 pages of addenda during the last six years of his life. The following quotation comes from page 60 of The Autobiography of Charles Darwin 1809-1882 published by his grandaughter Nora Barlow in 1958:

      ... ----Believing as I do that man in the distant future will be a far more perfect creature than he now is, it is an intolerable thought that he and all other sentient beings are doomed to complete annihilation after such long-continued slow progress. To those who fully admit the immortality of the human soul, the destruction of our world will not appear as dreadful. Another source of conviction in the existence of God, connected with the reason and not with the feelings, impresses me as having much more weight. This follows from the extreme difficulty or rather impossibility of conceiving this immense and wonderful universe, including man with his capacity of looking far backwards and far into futurity, as the result of blind chance or necessity. When thus reflecting I feel compelled to look to a First Cause having an intelligent mind in some degree analogous to that of man; and I deserve to be called a Theist."

  135. Many evolutionists are not atheists in any sense of the word. Some prefer to be called naturalists. Dr. Greg Graffin, lead singer of the punk band Bad Religion and coauthor of the book Anarchy Evolution (2010) has problems with the term "atheist."

      "It defines what someone is not rather than what someone is. It would be like calling me an a-instramentalist for Bad Reliogion rather than the band's singer. Defining yourself as against something says very little about what you are for. ...There's another problem with defining yourself in opposition to a particular worldview. Because atheism is defined through negation, it's never clear which meaning of "God" one opposes. Some believers revere an interventionist God who regularly influences physical events. Others believe that God rarely if ever exerts any influence over human affairs. Some people believe that God is evident in nature, while others believe that the existence of God can be revealed only through supernatural revelation. Many people believe in more than one god or even in a vaguely defined "spirituality" that does not require the existence of a specific god or gods."

  136. The development of life from self-replicating organic molecules in the original "primordial soup" is a scientific hypothesis called biopoiesis. Scientists have created the molecular building blocks of life from gasses in a primitive earth atmosphere. They have also created what appear to be the precursors of cells; however, the precise mechanism and biochemical pathway for biopoiesis remain hypothetical. If one hypothesis does not adequately explain the origin of life, this does not mean that an alternative hypothesis is necessarily true. In fact, there are several hypotheses for the origin of life on earth, including an extraterrestrial origin. One of these is called the panspermia hypothesis which states that the earth was "seeded" by extraterrestrial prokaryotic cells similar to archaebacteria that were carried to earth by meteors. Under a strict definition, a hypothesis must be testable and verifiable before it becomes a scientific theory. Will a scientific theory be developed to explain the origin of life? Only time will tell.

     See Archaebacteria: A Life Form On Mars? 

  137. In the classic spark discharge experiments by Stanley Miller and Harold Urey (1953 and 1959), amino acids were formed in a primitive, non-oxygen earth atmosphere containing water, methane, ammonia and hydrogen; however, the reducing atmospheric conditions used in this experiment are not consistent with the earth's primitive atmosphere (Kasting and Catling, 2003). Early earth probably had an atmosphere dominated by carbon dioxide like our neighboring planets Venus and Mars. Furthermore, it is is difficult to synthesize prebiotic compounds in a non-reducing atmosphere containing oxygen (R. Stribling and S.L. Miller, 1987). Another electric discharge mixture using hydrogen sulfide instead of hydrogen was tested by Miller in 1958 but never reported. Eric Parker and his colleagues analyzed this mixture in 2011 using state of the art high performance liquid chromatography and time-of-flight mass spectroscopy. Their test samples contained a large assortment of amino acids and amines, including numerous sulfur amino acids. According to Parker et al., the hydrogen sulfide gas mixture may not have been ubiquitous throughout the primitive atmosphere; however, it may have been prominent on a regional scale near volcanoes. Their results suggest that a mixture of oxidized and reduced gases, including hydrogen sulfide, may have aided the synthesis of amino acids and amines on the primitive earth.


    32. Alkaline Vents On The Ocean Bottom: Ideal Hatcheries For Life

  138. Biochemist Nick Lane discusses the origin of life in chapter one of his book Life Ascending: The Ten Great Inventions of Evolution (2009). According to Dr. Lane, the problem with the "primordial soup" described by other authors is that it is thermodynamically flat:

      "Nothing in the soup particularly wants to react, at least not in the way that hydrogen and oxygen want to react. There is no disequilibrium, no driving force to push life up, up, up the very steep energetic hill to the formation of truly complex polymers, such as proteins, lipids, polysaccharides, and most especially RNA and DNA. The idea that replicators like RNA were the first figments of life, predating any thermodynamic driving force, is, in Mike Russell's words, 'like removing the engine from an automobile and expecting the regulating computer to do the driving.' But if not from a soup, where did the engine come from?"

  139. Lane describes in detail a place where life on earth could have evolved: The mineral rich hydrothermal deep sea vents along oceanic rifts where all the precursors for biological molecules occur naturally, and where a plausible energy source exits to synthesize the polymers of life. Some of these vents have been called "black smokers" because of broiling metal sulphides welling up from the magma furnace below, reaching temperatures of 400 degrees Celsius before precipitating in the cold ocean waters.

  140. A second type of hydrothermal vent called "alkaline vent" has temperatures much more conducive to life. It was originally proposed by Mike Russel (see Russel & Martin, 2004). Unlike the acidic black smokers, this second type of vent arises from serpentine bedrock and is alkaline. It has a steady supply of hydrogen gas that reacts with carbon dioxide to form organic molecules. Microscopic examination reveals that these vent chimneys are composed of a labryinth of interconnecting compartments which retain and concentrate any organic molecules formed, making the assembly of polymers, like RNA, far more likely. Without the microscopic confines of micropores, newly formed monomers might disperse into the oceans and not polymerize into the macromolecules of life. In the early days of life, 4 billion years ago, the oceans were loaded with dissolved iron. According to Mark Lane (2009), "the microcompartments would have had catalytic walls, composed of iron-sulphur minerals, like the fossil vents at Tynagh, in Ireland. They would have worked, in fact, like natural flow reactors, with thermal and electrochemical gradients circulating reactive fluids through catalytic compartments."

      "A rocky labyrinth of mineral cells, lined with catalytic walls composed of iron, sulpur and nickel, and energized by natural proton gradients. The first life was a porous rock that generated complex molecules and energy, right up to the formation of proteins and DNA itself."

  141. Mark Lane refers to electrochemical gradients many times in his book. This may be defined as ions (usually protons) moving across membranes. A simplified explanation is the production of energy from anaerobic methane bacteria (Archaea): The electrons and H+ ions (protons) from hydrogen gas are used to reduce carbon dioxide (CO2) to methane (CH4). In the reaction, the H+ ions combine with the oxygen from CO2 to form water (H2O). During this process, the electrons are shuttled through an anaerobic electron transport system within the bacterial membrane which results in the phosphorylation of ADP (adenosine diphosphate) to form ATP (adenosine triphosphate). ATP is the vital energy molecule of all living systems which is absolutely necessary for key biochemical reactions within the cells. In fact, varnish bacteria living on sun-baked boulders make their ATP in a similar fashion, only the electrons are coming from the aerobic oxidation of iron and manganese. During the oxidation process, the electrons are shuttled through an iron-containing cytochrome enzyme system on the inner bacterial membrane. The actual synthesis of ATP from the coupling of ADP (adenosine diphosphate) with phosphate (PO4) is a lot more complicated and involves a mechanism called chemiosmosis. The electron flow generates a higher concentration (charge) of positively-charged hydrogen (H+) ions (or protons) on one side of the membrane. When one side of the membrane is sufficiently "charged," these protons recross the membrane through special channels (pores) containing the enzyme ATP synthetase, as molecules of ATP are produced. In eukaryotic cells, including the cells of your body, ATP is produced by a similar process within special membrane-bound organelles called mitochondria. In fact, some biologists believe that mitochondria (and chloroplasts) within eukaryotic animal and plant cells may have originated from ancient symbiotic bacteria that were once captured by other cells in the distant geologic past. This fascinating idea called the "Endosymbiont Hypothesis was originally proposed by Lynn Margulis. See Acquiring Genomes: A Theory of the Origins of Species by L. Margulis and D. Sagan (2002).

  142. Alkaline vents have the raw materials and necessary electrochemical gradients (proton gradients) for most of the above biochemical reactions of life. The electrochemical gradient between the alkaline vent fluid and the acidic seawater leads to the spontaneous formation of acetyl phosphate and pyrophosphate, which act just like adenosine triphosphate (ATP), the chemical that powers all living cells. These molecules drove the formation of amino acids--the building blocks of proteins, and nucleotides--the building blocks of DNA and RNA. According to Nick Lane and other researchers, life is inevitable on planets with oceans of acidic water and alkaline vents during millions of years of natural selection.

    When phosphates are transferred to other molecules, a process known as phosphorylation, the phosphorylated molecules have a much lower activation energy and react at lower temperatures. This is how all of the remarkable biochemical reactions can occur within cells of your body. For example, the relatively stable glucose molecule becomes glucose-phosphate during cellular respiration. It becomes more reactive and can be enzymatically broken down into carbon dioxide and water within seconds, thus releasing its electrons into the cytochrome enzyme system (electron transport) within mitochondria. Phosphate donors like acetyl phosphate and pyrophosphate must have occured early in the origin of life in order to produce complex macromolecules.

    See Archaebacteria: A Life Form On Mars?
      More About ATP: Colorful Structural Formula  

    Serpentine (technically called serpentinite) is a greenish, shiny rock that is exposed throughout the Coast Ranges of central and northern California, and the Sierra Nevada foothills. The name is derived from its resemblance to a snake skin. According to the California Geological Survey, serpentinite has been designated California's official state rock. Serpentinite is a magnesium silicate rock with a waxy luster and a shiny, marblelike appearance. It varies from cream white through all shades of green to black. Higher grade, deeply-colored serpentinites are used for animal carvings, particularly in Africa. Some polished serpentinites resemble jade in color and are used in pendants and rings.

    Serpentinite is formed on the sea floor at tectonic plate boundaries by a process called serpentinization: A hydration and metamorphic transformation of untramafic (igneous) rock from the Earth's mantle. This is a geological low-temperature metamorphic process involving heat and water in which low-silica mafic and untramafic rocks are oxidized (anaerobic oxidation of Fe 2+ by the protons of water leading to the formation of hydrogen gas) and hydrolyzed with water into serpentinite. It is only seen on land in subduction zones where oceanic rocks are preserved. Serpentinite is low in plant nutrients and high in toxic metals. Serpentinite outcrops in California often contain many species of rare endemic plants adapted to this rock type, including several species of cypress (Cupressus = Hesperocyparis).

      Serpentine & California Cypress (Hesperocyparis)  

  143. Nick Lane has published several scholarly articles on the origin of life in alkaline vents, including "Bioenergetics and the Probability of Life" (Journal of Cosmology Volume 10, 2010). A detailed discussion of his paper is beyond the scope of this page on evolution. The following summary is quoted from his article with Michael Le Page in New Scientist (14 October 2009):

    How Life Evolved: 10 Steps to the First Cells
    by Nick Lane and Michael Le Page (14 October 2009)

    1. "Water percolated down into newly formed rock under the seafloor, where it reacted with minerals such as olivine, producing a warm alkaline fluid rich in hydrogen gas, sulphides and other chemicals - a process called serpentinisation. This hot fluid welled up at alkaline hydrothermal vents like those at the Lost City, a vent system discovered near the Mid-Atlantic Ridge in 2000."

    2. "Unlike today's seas, the early ocean was acidic and rich in dissolved iron and carbon duioxide. When upwelling hydrothermal fluids reacted with this primordial seawater, they produced carbonate rocks riddled with tiny pores and a "foam" of iron-sulphur bubbles."

    3. "Inside the iron-sulphur bubbles, hydrogen reacted with carbon dioxide, forming simple organic molecules such as methane, formate and acetate. Some of these reactions were catalysed by the iron-sulphur minerals. Similar iron-sulphur catalysts are still found at the heart of many proteins today."

    4. "The electrochemical gradient between the alkaline vent fluid and the acidic seawater leads to the spontaneous formation of acetyl phosphate and pyrophospate, which act just like adenosine triphosphate or ATP, the chemical that powers living cells. These molecules drove the formation of amino acids--the building blocks of proteins--and nucleotides, the building blocks for RNA and DNA."

    5. "Thermal currents and diffusion within the vent pores concentrated larger molecules like nucleotides, driving the formation of RNA and DNA--and providing an ideal setting for their evolution into the world of DNA and proteins. Evolution got under way, with sets of molecules capable of producing more of themselves starting to dominate."

    6. "Fatty molecules coated the iron-sulphur froth and spontaneously formed cell-like bubbles. Some of these bubbles would have enclosed self-replicating sets of molecules--the first organic cells. The earliest protocells may have been elusive entities, though, often dissolving and reforming as they circulated within the vents."

    7. "The evolution of an enzyme called pyrophosphatase, which catalyses the production of pyrophosphate, allowed the protocells to extract more energy from the gradient between the alkaline vent fluid and the acidic ocean. This ancient enzyme is still found in many bacteria and archaea, the first two branches on the tree of life."

    8. "Some protocells started using ATP as well as acetyl phosphate and pyrophosphate. The production of ATP using energy from the electrochemical gradient is perfected with the evolution of the enzyme ATP synthase, found within all life today."

    9. "Protocells further from the main vent axis, where the natural electrochemical gradient is weaker, started to generate their own gradient by pumping protons across their membranes, using the energy released when carbon dioxide reacts with hydrogen. This reaction yields only a small amount of energy, not enough to make ATP. By repeating the reaction and storing the energy in the form of an electrochemical gradient, however, protocells "saved up" enough energy for ATP production."

    10. "Once protocells could generate their own electrochemical gradient, they were no longer tied to the vents. Cells left the vents on two separate occasions, with one exodus giving rise to bacteria and the other to archaea."


    Building Blocks Of DNA From Outer Space?

  144. One of the most interesting pieces of evidence for an extraterrestrial origin of complex biological molecules is the discovery of DNA bases (nucleobases) in carbon-rich meteorites (carbonaceous chondrites) from Antarctica. According to Dr. Michael Callahan of NASA's Goddard Space Flight Center (2011): "For the first time, we have three lines of evidence that together give us confidence these DNA building blocks actually were created in space." Callahan is lead author of a paper on the discovery appearing in Proceedings of the National Academy of Sciences, 2011. Extracts from carbon-rich meteorites were analyzed by liquid chromatography and mass spectrometry to determinine the chemical compounds and their stuctural formulas. Adenine and guanine, two of the four DNA bases of life, were isolated plus a variety of nucleobase analogs not found in living organisms. These nucleobase analogs are important because they would not be expected from terrestrial contamination. In fact, none of them were found in the nearby ice. The well-studied Murchison meteorite in Australia also contained nucleobase analogs and over 100 amino acids (Zita Martins, et al. 2008). These nucleobases were synthesized in non-biological reactions in the laboratory from chemicals present in asteroids, including hydrogen cyanide, ammonia and water. According to N. Lane, J. Allen and W. Martin (2010), the presence of complex biological molecules in meteorites does not mean the life must have arisen in outer space.

    Meteorite fragment from Arizona and illustration of 4 DNA nucleobases: Adenine (C5H5N5), thymine (C5H6N2O2), cytosine (C4H5N3O) and guanine (C5H5N5O). For those counting atoms in the above molecules, each one is missing one green hydrogen because it is on the reverse side and not visible. Two purine bases, adenine and guanine, were found in carbon-rich Antarctic meteorites plus a variety of nucleobase analogs. If complex biological molecules were formed in space, were the building blocks for life on earth seeded from meteorites? It is intriguing to ponder DNA nucleobases (the rungs of DNA ladders) traveling through space inside meteorites!

    Simplified model of a small section of ladder-shaped DNA. The "rungs" are composed of nucleobase pairs. Adenine (A) always pairs with thymine (T) and guanine (G) always pairs with cytosine (C). The "rails" are composed of alternating phosphates (P) and deoxyribose sugars (D). Although some people doubt whether these chemicals could have formed in a primitive earth atmosphere, nucleobases have been discovered in carbon-rich meteorites that reached the earth.

     The Structure & Function of DNA 
    PCR: Polymerase Chain Reaction


    33. The Danger Of Imposing Non-Science Dogma In Science Courses

  145. Advocates of intelligent design would like to see their dogma taught alongside evolution in science courses. As I have stated in this report, intelligent design is not a scientific theory. It is not based on empirical evidence and cannot be tested or proven. It is dangerous to impose non-scientific dogma in science courses. One case in point is the teaching of acquired characteristics in the Soviet Union between 1948 and 1964. This hypothesis was proposed by the French biologist Jean-Baptiste de Lamarck in the early 1800s, and was actually proposed thousands of years earlier by Greek scholars. According to acquired characteristics, the environment can bring about inherited change. One classic example given by Lamarck is that the long neck of the giraffe developed over time because animals stretched their necks to browse high in trees and then passed on the propensity for a longer neck to their offspring. Although the environment is a factor in evolution, the mechanism of acquired characteristics has been thoroughly disproved during the last century: Phenotypic changes acquired during an organism's lifetime do not result in genetic changes that can be passed to subsequent generations. Potential gene-bearing gametes are set aside in the form of mother cells (oocytes and spermatocytes) early in an animal's embryonic development. The long neck of the giraffe is explained by genetic variabilty and selection for longer-necked offspring over thousands of generations. By the mid 1800s both Charles Darwin and Alfred Russel Wallace independently came up with their hypotheses of "survival of the fittest" to explain the origin of species by natural selection; but it was the Austrian Monk Gregor Mendel who in 1865 first described a mechanism to explain variability and the transmission of traits from parents to offspring. The story behind the teaching of acquired characteristics in the Soviet Union is a good example of why politics and religion should not interfere with scientific research.

    Evolution of the giraffe's long neck is still debated by authorities. The giraffe doesn't have special genes for a long neck. Like the mouse, genes controlling neck growth during embryonic development may be switched on for a longer time, so the giraffe ends up with a longer neck. As Richard Dawkins points out in his book Climbing Mount Improbable (1996), the long neck of a giraffe doesn't require a macromutation. There are two main hypotheses for the origin of long necks. 1. Giraffes have a competitive advantage in reaching higher foliage that is out of reach for other browsing herbivores; however, research indicates that giraffes also feed on lower branches (at or below shoulder height) during the drought season when browsing competition should be the highest. 2. The long neck evolved as a result of sexual selection (R.E. Simmons and L. Scheepers, 1996). Long-necked males have an advantage in "necking" when they strike a male opponent with their head. The winner of these duels has greater access to a female in estrus. Longer necks and heavier heads of males may be an advantage in "necking," but it doesn't explain the long necks of female giraffes (G. Mitchell, S.J. van Sittert and J.D. Skinner, 2009).

  146. In 1948, a decree of the Presidium of the Soviet Academy of Sciences appeared in Pravda. It stated that communists must teach and say that acquired characteristics are inherited. All research in agriculture and biology was controlled by Trofim Lysenko, the "dictator of genetic research." Refusal to follow acquired characteristics resulted in the dismissal, exile and execution of a number of Russian geneticists. During the late 1940s and 1950s, the Soviet Union fell behind the rest of the world in genetics research and there was a gradual failure in Soviet agriculture. Shortly after the downfall of Nikita Kruschev in 1964, Lysenko was dismissed from his administrative position. Soviet research in acquired characteristics was exposed as a fraud and the translation of western textbooks containing Mendelian genetics was ordered. The imposition of non-scientific dogma in the Soviet Union for a period of almost two decades resulted in a missing generation of trained geneticists. Politics and religion should not interfere with scientific research or the teaching of science in our schools.

  147. As I have stated above in this essay, the K-12 general biology supplement Of Pandas and People contains some misleading information. It also makes some very simplistic comparisons that are inappropriate for an academic science course designed to prepare young minds for the future of science and technology. For example, if we see the words "John Loves Mary" written in the sand, we know that this message was written by an intelligent designer called Homo sapiens sapiens. Then why can't a message written in the DNA of our genes also be made by an intelligent designer? This is another example of an oversimplified comparison. We know from experience that people write messages in the sand. Probably everyone has done this at one time in their life. But we can only hypothesize about the origin of coded messages in DNA, or for that matter, the origin of DNA. We can say that DNA is so marvelous and complex that is must have come from an intelligent designer, but now we are basing our conclusion on faith, not science. That is why intelligent design does not belong in a science class. Although proponents of intelligent design are very careful not to specify who their "designer" is, the logical conclusion is that it must be God. We have freedom of religion in the United States guaranteed by the First Amendment of the Constitution. It is not wrong to believe that our God is the intelligent designer; however, explanations of the natural world based on faith just don't belong in a science class.

  148. During the famous Dover School Board Trial of fall 2005, proponents of intelligent design argued that their "theory" was not based on biblical creationism. They even claimed that their recommended supplemental biology textbook Of Pandas and People (2nd. Edition, 2004) did not center around creationism. The latter testimony was repudiated by Dr. Barbara Forest after she discovered early drafts of the textbook with the words "creation" instead of intelligent design. In one draft (pp. 3-41), the word "creationists" was incompletely replaced by the words "intelligent design." It is clear that intelligent design is synonymous with creationism.

    Biology and Creation (1986): Evolutionists think the former is correct, creationists accept the latter view."

    Biology and Origins (1987): Evolutionists think the former is correct, creationists accept the latter view."

    Of Pandas and People (1987): Evolutionists think the former is correct, creationists accept the latter view."

    Of Pandas and People (1987): Evolutionists think the former is correct, cdesign proponentsists accept the latter view."

  149. The Biophysical Society is an international society of scientists established to encourage development and dissemination of knowledge in biophysics. The following comes from their concluding paragraph regarding the teaching of alternatives to evolution in K-12 science classrooms (November 5, 2005): "Attempts to suppress or compromise the teaching of evolutionary science in the United States are misguided actions that will deprive our youth of a clear understanding of the scientific process, and of the scientific skills that they need to compete in a global economy: one that is increasingly driven by science and technology. Moreover, current efforts to disguise theology as science do a severe disservice to the scientific profession and to the people of the United States."

  150. Since intelligent design is not science, it does not belong in the science curricula of the nation's primary and secondary schools. This is the position statement of the following prestigious scientific organizations: National Academy of Sciences, American Association for the Advancement of Science, National Science Teachers' Association, American Geophysical Union, American Chemical Society, American Association of Physics Teachers, and the American Astronomical Society. All of these organizations emphasize the importance of scientific methodology as well as articulating well-established scientific theories.

    See DNA Structure & Function
     See Polymerase Chain Reaction 


    34. Evolution Of Macromolecules & Cells by Random Probability

  151. Some authors have used the extrapolation of Darwin's Origin of a Species by Means of Natural Selection to include the first macromolecules and living cells, although this has never been proven through rigorous scientific analysis. They have even speculated that macromolecules and living cells evolved purely by random chance. A functional protein may contain more than 500 amino acids arranged in a specific orderly sequence with a unique 3-dimensional structure. The probability for the 2-dimensional arrangement of 500 amino acids is astronomical. It is equivalent to 1 in 20500 or roughly 1 in 10650. Some models of the visible universe list 1080 for the total number of subatomic particles (or electrons), depending on the reference. William A. Dembski, a staunch proponent of intelligent design has come up with his universal probability bound, a numerical value that gauges the likelihood that a given event could have occurred by chance in nature, or whether it occurred by intelligent design (i.e. by a natural or supernatural intelligence). Dembski's probability bound is a cutoff point between probability and a "creator." It is based on a very improbable number (1 in 10150), derived from the inverse of the product of several astronomical numbers, including the number of subatomic particles in the universe. Whether this number is the cutoff point between random probability and a creator is impossible to prove. For an intelligent review of Dembski's mathematical explanation for intelligent design, please read "The Dream World of William Dembski's Creationism" by Mark Perakh in Skeptic Volume 11 (Number 4) 2005, pages 54-65.

     See Dembski's Universal Probability Bound 

  152. Given the plausible conditions and energy forces of a primitive earth atmosphere, the origin of life was probably a lot more likely than simple random probability. Some of these "natural" conditions and forces may have included biological compounds in a "primordial soup," possibly seeded by carbon-rich meteorites; shallow pools lined with clay particles bearing electrostatic charges; heat and electrical discharges (lightning); and a time window of countless million of years. Whether a supernatural force was also involved in this process is perhaps one of the most controversial topics ever discussed by educated people.


    35. Did All Life On Earth Evolve From A Common Ancestor?

  153. All life on earth is determined by the same genetic code consisting of the four bases Adenine, Guanine, Cytosine and Thymine. The fact that we also share some of the same DNA sequences (genes) as eukaryotic cells is strong evidence that we are all related. The probability that identical genes evolved independently in diverse organisms is mathematically too unlikely. The following explanation is summarized from Eric Roston's fascinating book entitled The Carbon Age. The thermophilic bacterium Aquifex aeolicus lives in hot springs at Yellowstone National Park in water that is nearly boiling at 95° C (203° F). This rod-shaped bacterium 5 micrometers in length has a genome containing 1,551,335 base pairs. Since each base pair has four possible arrangements (see paragraph #15 above), the total number of different DNA combinations for this minute organism is 41,551,335. Thats four multiplied by itself 1,551,335 times. Compare this number with 1080 or 4133, the total number of electrons in some models of the visible universe. The DNA in a human nucleus contains at least three billion base pairs or 4 3,000,000,000 different sequences. "These numbers are so preposterously large that the likelihood for random overlap is all but mathematically zero. So if human beings and A. aeolicus have any genes--just one--in common, they are not random, and humans and A. aeolicus share a genetic code descended from a single ancestor." In fact, we actually share several dozen genes with A. aeolicus.

    A boiling hot spring in Yellowstone National Park containing Aquifex aeolicus, photosynthetic cyanobacteria, and Thermus aquaticus, a heterotrophic bacterium that survives on minute amounts of organic matter in the water. The latter species is the original source of TAQ polymerase used in the amplification of DNA using the polymerase chain reaction (PCR). Scientists from throughout the world are studying the amazing bacteria flora at Yellowstone National Park. This is one of the best places on earth to study these organisms in their natural protected habitats. In other parts of the world, similar hot springs have been destroyed for the production of geothermal energy. Life as we know it may have first arisen more than three billion years ago in a high temperature environment of boiling water. Thermophilic bacteria in hot springs of Yellowstone National Park may be relict populations of the first life on earth. In fact, these thermophilic bacteria may be the ancestors of all other life forms, including humans.

     Wayne's Word Article About Polymerase Chain Reaction 
    See The Wayne's Word Table Of Cell Size Comparisons


    36. Addendum: Origin Of The Magnificent Grand Canyon

  154. Standing on the rim of this enormous canyon and gazing out at the colorful strata representing over a billion years of geologic time, you realize the brief life span of a mortal human. Was this magnificent canyon created in its present form by God, or was it formed during millions of years of sedimentation, uplifting and erosion? If it was underwater during the worldwide biblical flood, how did all the animals become stratified into layers dating back to the Cambrian period over 500 million years ago? Were all these creatures treading water at the same time during the great flood, only to die and settle out in layers?

  155. Fossil evidence indicates that numerous species of animals lived during different periods of time. As layers of sediments were deposited, animals from each time period were recorded in the strata as fossils. About 40-70 million years ago, the Grand Canyon region was uplifted into a high plateau during a tremendous mountain building era known as the Laramide Orogeny. This massive uplifting gave rise to the Rocky Mountains and the origin of the Colorado River drainage. During the past six million years, the Colorado River has cut through this high plateau region, as it winds its way to the low Colorado Desert and eventually to the Gulf of California. The river's steep gradient of 8 feet per mile (1.5 m per km) and high sediment load contributed to its cutting power. Rockfalls, landslides, flash floods from torrential rains, and ongoing erosion in tributary canyons, have worked in tandem with the Colorado River to widen the canyon and form the intricate cliff and slope pattern seen today.

    Trilobites such as these Elrathia kingi from Utah lived in shallow Cambrian seas. Trilobite fossils are also present in the lower sedimentary strata of the Grand Canyon. They are often placed in the class Trilobita within the phylum Arthropoda. They flourished during the Cambrian period over 500 million years ago. The last of the trilobites disappeared in the mass extinction at the end of the Permian, about 250 million years ago. They are a famous and well-known fossil group, possibly second only to the dinosaurs.

  156. There is overwhelming evidence from paleontology and geology that the Grand Canyon's strata and all of its ancient life evolved during the past 550 million years. To suggest that it was created in its present form, or that all of this occurred during the last 6,000 years as stated in the Bible, is based purely on faith. Some people with a much broader interpretation of the Bible believe their faith does not conflict with the objective scientific evidence.


    37. True or False Summary Statements

    1. A scientific theory is an explanation for the cause or causes of complex natural phenomena based on observable facts and rigorous tests that have been repeatedly verified by scientists.

    2. Scientific theories are generally more complex and dynamic than scientific laws, and they may be changed as the body of experimental data and analysis develops.

    3. Scientific laws are strictly empirical and explain a single action or set of actions; they can sometimes be expressed in terms of a single mathematical equation.

    4. Hypotheses are tentative explanations or propositions about the causes of natural phenomena; they are not elevated to the status of scientific theories and scientific laws without rigorous testing and review by scientists.

    5. Scientific theories and scientific laws both start out as hypotheses that have been repeatedly tested by scientists and have survived.

    6. A scientific theory is a set of statements, including scientific laws, that has been tested repeatedly on new data; it is not subordinate to, or lesser than, a scientific law.

    7. A scientific theory is not "just a theory," it is as good as it gets when it comes to explaining complex natural phenomena.

    8. Dynamic scientific theories do not necessarily become scientific laws; along with scientific laws they are the foundations of scientific knowledge and together explain our complex natural world.

    9. True scientific theories have been developed through the rigorous scientific method; they are much different from "common theories" that are used by laypersons and creationists.

    10. Most common theories are only educated guesses; at best they are only tentative hypotheses

    11. The "endosymbiont theory" should be called the "endosymbiont hypothesis."

    12. Symbiogenesis is technically a scientific hypothesis rather than a scientific theory.

    13. Some scientists incorrectly use the term "theory" to explain phenomena that has not been repeatedly tested and verified by the scientific method.

    14. One scientist cannot create a scientific theory.

    15. A scientific theory should not be called a fact.

    16. It is still Einstein's "theory of relativity," even though it is probably as close to a fact as anyone can get in science. Even though it has survived the test of time and has passed all tests so far, it is still subject to challenge as the body of experimental data and analysis develops.

    17. A common or layperson's theory is equivalent to an educated guess or hunch.

    18. All facts in science are provisional and subject to challenge.

    19. The scientific theory of evolution assumes the existence of life and is directed to an explanation of how life evolved.

    20. The scientific theory of evolution does not deal with the origin of life, and it does not presuppose the absence of a creator or God.

    21. Scientific explanations for the origin of life are more properly referred to as hypotheses rather than scientific theories.

    22. Intelligent design is a non-scientific (non-testable) argument or assertion that life owes its origin to a master intellect.

    23. According to creationists, all life originated abruptly in its present form.

    24. Faith is the belief in the existence of something without proof or verifiable empirical evidence.

    25. Politics and religion should not interfere with scientific research or the teaching of science in our schools.

    26. The existence of true coconut pearls is based on faith rather than empirical evidence.

    27. Intelligent design as the only alternative to evolution is a false dichotomous argument.

    28. The argument whether evolution is a theory or a fact is an invalid comparison.

    29. The evidence showing that life evolved on this planet is overwhelming; however, the exact mechanism for the origin of life is hypothetical.

    30. Biopoiesis is a scientific hypothesis for the origin of life from self-replicating organic molecules in the original "primordial soup."

    31. Panspermia is a hypothesis which states that the earth was "seeded" by extraterrestrial prokaryotic cells similar to archaebacteria that were carried to earth by meteors.

    32. Natural selection is a well-tested and verifiable mechanism to explain the origin of species according to the scientific theory of evolution.

    33. Genetic variability is the raw material for evolution.

    34. The evolution of many species in a new habitat from an ancestral species is called adaptive radiation.

    35. The remarkable "Silver Sword Alliance" and the unusual lobelioids on the Hawaiian Islands is a good example of adaptive radiation.

    36. The word "theory" is commonly used by scientists and lay people for tentative explanations that have not been universally tested and accepted by the scientific community. In this case, the term hypothesis is more appropriate.

    37. The word "theory" is commonly used by scientists and lay people for explanations that have been repeatedly verified and universally accepted by the scientific community. In this case, the term scientific theory is more appropriate.

    38. The African euphorbias and North American cacti are classic examples of convergent evolution.

    39. Parallel evolution is similar to convergent evolution, except the organisms being compared may not have an overall resemble to each other.

    40. The noun "theory" associated with time-tested explanations such as evolution, relativity and plate tectonics, should be modified by the adjective "scientific" in order to distinguish it from a "common" or "layman" theory that is essentially a tentative explanation or untested hypothesis.

    41. Using the term homoplasy avoids the confusing distinction between parallel and convergent evolution.

    42. The origin of the eye is different phyla of animals is probably not a good example of homoplasy.

    43. Humans once had 24 pairs of chromosomes like present-day great apes (orangutans, gorillas and chimpanzees).

    44. Contrary to anti-evolution propaganda, there are many excellent examples of "missing links" in the fossil record, evolutionary transitions between distantly related animal groups.

    45. Fossils known as "missing links" represent major phylogenetic branches (clades) giving rise to successive levels of life on earth.

    46. Evolution is best explained as a well-established scientific theory based on numerous facts.

    47. Evolution can also be referred to as a fact according the definition of fact in the Merriam-Webster Unabridged Dictionary of the English Language.

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