The Theory of Life: Evolution

Okay, to hold you guys over until I can finish part three, I figured I would post a paper I wrote last year for my college Biology class. I took the class at Franklin University in Columbus, Ohio, a secular university.
The questions in bold were what I had to answer for the paper, and I gave a strictly scientific response to each question. You will not find anything about God or the Bible in this report. 
I used several peer-reviewed sources and frequent in-text citations, so you can be assured that none of the facts presented have been made up. 
It is rather academic, but if you like academic papers, then you should find this interesting.
 Human Evolution
A popularized view


A more contemporary view


“Yes, what you see there is the complete Darwinian view of human origins, the complete package… The Darwinian picture has a long tradition and is very powerful.” David Pilbeam – Yale University Paleoanthropologist
“Darwin’s theory of evolution is often said to be protected by walls that are at least seven miles thick, in that it is not only true, but unassailable. It is a considerable irony, therefore, that some of the most cogent criticisms of Darwin’s theory are the result of work undertaken by very orthodox members of the biological establishment itself. Such criticisms are inevitably designated as calls for further research. They are, nonetheless, what they are.”– David Berlinski
How did we get here? Every guy and his cousin has an idea, but the dominant theory in the academic and scientific communities is the Theory of Evolution.
What is the scientific evidence to support evolution? Is there any scientific evidence against it?
            Much of the information presented as evidence in support of evolution can be classified into one of the following categories:  the fossil record, comparative embryonic anatomy, molecular biochemistry, and biogeography.
 The fossil record: The fossil record is credited as being one of the major sources supporting Evolution. Fossils, the preserved remnants of organisms, show us life forms that existed long ago (Johnson, 2010, p. 507). According to the Theory of Evolution, all life descended from a common ancestor, which “arose from the hot, steamy environment of Earth more than 3 billion years ago,” (Johnson, 2010, p. 507). Johnson describes what fossils are, provides information about how they are dated, states that the fossil record is incomplete and then simply asserts that the fossil record provides compelling evidence for evolution.  However, he does not actually provide a rationale for how the fossil record itself provides evidence in support of Evolution.
According to the evolutionary story, descent over time, genetic modification, and unpredictable and natural selection, caused all the diversity of life we see today. If this is true, we should see organisms slowly changing (evolving), over numerous generations, from one species into another. However, the fossil record shows no evidence of this happening. The lack of “transitional” forms in the fossil record is a significant problem for the Theory of Evolution; if organisms have been changing from one species to another for millions of years, there should be transitional, fossilized forms everywhere in the fossil record, but they are mysteriously absent. Instead, the fossil record shows complete, fully formed, species, and no transitioning from one species to another. “Additionally, the fossil record displays a regular pattern of abrupt appearances of new life forms (instead of their arrival by innumerable small steps in a Darwinian manner)…” (Lönnig, 2004). 

The “Cambrian Explosion” is an example of the fossil record that does not coincide with Evolution. The “Cambrian Explosion” is “the geologically sudden appearance of many new animal body plans about 530 million years ago. At this time, at least nineteen, and perhaps as many as thirty-five phyla of forty total (Meyer et al. 2003), made their first appearance on earth within a narrow five- to ten-million-year window of geologic time (Bowring et al. 1993, 1998a:1, 1998b:40; Kerr 1993; Monastersky 1993; Aris-Brosou & Yang 2003)” (Meyer, 2004).
The sudden appearance (geologically speaking) of the organisms of the Cambrian period, “implies the absence of clear transitional intermediate forms connecting Cambrian animals with simpler pre-Cambrian forms,” (Meyer, 2004).  “And, indeed, in almost all cases, the Cambrian animals have no clear morphological antecedents in earlier Vendian or Precambrian fauna (Miklos 1993, Erwin et al. 1997:132, Steiner & Reitner 2001, Conway Morris 2003b:510, Valentine et al. 2003:519-520).” (Meyer, 2004).  So not only does the Cambrian Explosion reveal a lack of transitional forms, but the Cambrian Explosion shows no clear variations between the animals of the Cambrian period and of the animals before the Cambrian period. In a 5 to 10 million year time frame, there should be a large amount of genetic variation and a plethora of transitional forms. There is neither. Evolutionary biologists continue to blame the lack of transitional forms on the incompleteness of the fossil record, however, it has been over 150 years since Darwin’s theory, and the missing fossils remain missing. Also, several recent discoveries and analyses suggest that the morphological gaps may not be merely a result of incomplete sampling of the fossil record (Foote 1997, Foote et al. 1999, Benton & Ayala 2003, Meyer et al. 2003), “suggesting that the fossil record is at least approximately reliable (Conway Morris 2003b:505),” (Meyer, 2004).
Living fossils have also been discovered time and time again. A living fossil is an organism that was once only known by its fossils. Scientists estimate that the creature had been extinct for millions of years, only to find the creature living and unchanged from its fossil. If creatures are evolving, what explains the presence of living fossils which have remained unchanged for millions upon millions of years?

coelacanth (Latimeria chalumnae) marine biologists hailed the fish as a “living fossil” – an animal that has existed virtually unchanged since it first appeared over 400 million years ago (BBC, 1999).
So while the fossil record is claimed to be a source supporting the Theory of Evolution, the fossil record actually poses significant problems for the theory.
Comparative embryonic anatomy: Another source that is used as evidence for the Theory of Evolution is the comparison of the “anatomy of animals and the development of their embryos,” (Johnson, 2010, p. 509). “Scientists describe anatomical structures as homologous, analogous, or vestigial,” (Johnson, 2010, p. 509). An example of this can be seen in the forelimbs of all vertebrates. All vertebrates seem to share nearly the same set of bones which are arranged in similar patterns. Homologous structures are body parts that are thought to have the same origin. Analogous structures share a common function but are not necessarily thought to have common ancestry (Johnson, 2010, p. 509). Since many animals seem to share common characteristics (similar bone structure), we can conclude that life had some kind of common origin, however, since the fossil record does not show a descending from one to another, we cannot scientifically know exactly what the cause is for the physical similarities we see between life forms.
Vestigial structures are thought to serve little to no function at all. Vestigial structures can be considered homologous to body parts in other animals, where they still serve an important function (Johnson, 2010, p. 509). The human tailbone (coccyx) is thought to be the remains of a tail, which leads scientists to conclude we share ancestry with other vertebrates with tails (Johnson, 2010, p. 509). However, the more we learn about the human body the more our “vestigial” structures turn out to not be vestigial after all. The human pinky toes, tonsils, and appendix were once thought to serve no purpose.  We now know that tonsils and the appendix play an important part in the immune system and pinky toes help us keep our balance while also helping to disperse impact throughout the foot when we run (Wolchover, 2011). Likewise, the tailbone is also now known to have an important function. The coccyx “is an attachment point of a number of muscles at the pelvis. We need it for upright locomotion. It would be catastrophic if it went away,”—Kenneth Saladin, anatomist and physiologist at Georgia College and State University (Wolchover, 2011). Just because our spinal cord extends slightly below the pelvis does not mean we can conclude that we shared ancestry with vertebrates with tails. This assertion must be backed up with scientific observation if we are to make this conclusion.
What is natural selection, and how does the process work? How does natural selection contribute to evolution?
                      Natural selection, described by Darwin as “survival of the fittest” is the process by which organisms adapt to their environment by developing certain traits over time that enable their survival in a particular geographic region. It is also described as the process of random genetic variances that cause differentiation between organisms. It is also thought that natural selection combined with random mutations cause the change of one species into another. The organisms which receive beneficial mutations will survive to reproduce, while the organisms which receive negative mutations will die out. Individuals with certain traits are more fit for their local environment and therefore are more likely to survive and reproduce (survival of the fittest). Mutations with the addition of natural selection contribute to changes in the gene pool of a population. This is the process of natural selection (Johnson, 2010, p. 512).

            Natural selection contributes to evolution because over time natural selection causes some genes to fade away, while others become prominent. Since genes influence a population’s physical traits and functions, the changing of the genes likewise causes populations to change. We have directly observed evidence of natural selection and can even control the process. Genetic engineering is an example of how humans can control natural selection. Changes within a species are scientifically observable. However, we have not been able to engineer a completely new species, nor have we directly or scientifically observed a species evolving to become a completely different species. A 2008 article in Trends in Ecology and Evolution acknowledged the existence of a ‘healthy debate concerning the sufficiency of neo-Darwinian theory to explain macroevolution.  It is debated whether natural selection is actually the cause of changes that give rise to new species, or whether natural selection only plays a part in adaptation within existing species.Biologist Stewart Newman argued, ‘You can’t deny the force of selection in genetic evolution … but in my view this is stabilizing and fine-tuning forms that originate due to other processes.’”
“… it comes as something of a surprise to learn that despite very long-standing claims by evolutionary biologists to have established the robust viability of natural selection as a biological force, the overwhelming number of such studies have been conducted only in the past fifteen years.” (Berlinski, 2005).
What were the first life-forms on Earth?
            In today’s world the formation of organic molecules requires enzymes, but enzymes had not yet evolved at the time life was first recorded (Johnson, 2010, p. 514). How could organic molecules have formed without enzymes if science has never observed organic molecules forming without them? According to Johnson, the conditions of the early Earth were such that it was possible for organic molecules to form without the presence of enzymes.  Johnson does not present any scientific data to support such a theory, but allows himself to speculate on how this could have happened. “Apparently the intense heat, ultraviolet radiation, and electrical discharges produced an extreme amount of energy, enough to combine molecules in the atmosphere into simple organic compounds, even without enzymes” (Johnson, 2010, p. 514). So scientists are not exactly sure how this was possible, but they know that life formed. Professor Edwin Conklin stated, “The probability of life originating from accident is comparable to the probability of the Unabridged Dictionary resulting from an explosion in a printing shop.”
            Eventually, scientists believe that non-living organic material was able to mix together in Earth’s primordial oceans and spontaneously transform from non-living to living. The first living organisms must have been anaerobic because there was believed to be no oxygen in Earth’s early atmosphere. Scientists approximate that at about 3 billion years ago, certain cells had advanced to the point that they were able to carry out the process of photosynthesis, as a result of random mutations (Johnson, 2010, p. 515).   
How did photosynthetic organisms affect evolution?
            Scientists believe that the formation of photosynthetic organisms created an abundance of oxygen in Earth’s atmosphere, which gave rise to the evolution of oxygen breathing (aerobic) organisms (Johnson, 2010, p. 515).
Who were the first hominids? What did they look like?
          The first hominids were believed to come from Africa. Scientists disagree regarding dates, classification of fossils, and the general framework of human evolution. However, human evolution is fairly well established (Johnson, 2010, p. 517).
Australopithecus afarensis: One of the first hominids to appear was Australopithecus (southern ape). The fragments of an Australopithecus skeleton was found in Ethiopia in 1974 (Lucy), and is the only one still considered (scientists disagree) to be a candidate as a human ancestor. These hominids were short (about a meter tall) with arms long relative to their bodies.

Homo habilis: Homo habilis was thought to be our first distinctly human ancestor, however, new fossil discoveries in Africa cloud our view of human evolution. Homo habilis is no longer thought to be in the genus ‘Homo.’ “The old theory was that the first and oldest species in our family tree, Homo habilis, evolved into Homo erectus, which then became us, Homo sapiens. But those two earlier species lived side-by-side about 1.5 million years ago in parts of Kenya for at least half a million years, Leakey and colleagues report in a paper published in Thursday’s journal Nature. In 2000 Leakey found an old H. erectus complete skull within walking distance of an upper jaw of the H. habilis, and both dated from the same general time period. That makes it unlikely that H. erectus evolved from H. habilis, researchers said.” (Smith, 2007).
Homo erectus: More human-looking, Homo erectus was thought to have arisen from Homo habilis, but we now know that they were living at the same time (see above). Homo erectus is considered a contemporary with modern humans due to its large brain size and ability to walk upright (Johnson, 2010, p. 518).
 “I have come to believe that many statements we make about the hows and whys of human evolution say as much about us, the paleoanthropologists and the larger society in which we live, as about anything that ‘really’ happened.” David Pilbeam Yale University Paleoanthropologist
            The dominant theory of life’s origins within the academic and scientific communities is commonly referred to as Neo-Darwinian Evolution.  However, statements in Biology textbooks that represent Evolution, meaning Neo-Darwinian Evolution, as being universally accepted by “scientists” are misleading. There is a significant amount of skepticism in the scientific community surrounding the theory of Neo-Darwinian Evolution.  Over the years, a number of alternatives to the Darwinian Theory of Evolution have been proposed, including punctuated equilibrium, self-organization, structuralism, and intelligent design. In 2001, The Discovery Institute drafted a statement entitled “A Scientific Dissent from Darwin.”  When first published, the statement was endorsed by 100 scientists.  Last updated in 2010, the statement now contains the signatures of over 700 scientists.

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Johnson, M. D. (2010). Human biology:  concepts and current issues (5th ed.). San Francisco: Benjamin Cummings.
Luskin, C., Sciences), M. (., & J.D.. (n.d.). Response to the NCSE’s Reply to Explore Evolution on Natural Selection (Explore Evolution – Further Debate). Explore Evolution | Discussion | Ongoing Debate. Retrieved April 8, 2011, from
Meyer, S. (n.d.). Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories. discovery. Retrieved April 6, 2011, from
Smith, A. (n.d.). Paleoanthropologists Disown Homo habilis from Our Direct Family Tree – Evolution News & Views. Evolution News & Views. Retrieved April 7, 2011, from
Wolchover, N. (n.d.). FYI: When Will We Evolve Out Of Our Useless Appendages? | Popular Science. Popular Science | New Technology, Science News, The Future Now. Retrieved April 7, 2011, from

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