Origins
Darwin and Pandora
Charles Darwin, like Pandora, opened a world of trouble that upset the established order of things, especially for religious fundamentalists believing in a literal interpretation of the Genesis creation.
Fundamentalists have convinced themselves that Evolution is “a theory in crisis”, on “the brink of destruction.” These people possess no understanding of actual scientific thought, evidence, and methods.
The current state of the Evolutionary Theory is the same one that it has been in for years: Evolution is both a theory and a fact.
In everyday non-scientific parlance, the term “theory” refers to a simple guess or information that is “imperfect,” and a “fact” is irrefutable truth. In science, each of these words take on entirely different meanings. In science, facts are simply hard data derived from observations, and do not necessarily translate to “truth”‘ or “absolutely certainty.” Rather, a fact is simply data that has been confirmed to a point where rejecting it would be absurd. Theories are sets of ideas structured to interpret the facts and how they fit together as a whole. They are used to describe mechanisms that unite factual information. Theories, as opposed to a simple hypothesis, have withstood the test of time and are supported by vast amounts of observational evidence.
Evolution is both a fact and a theory. It is a fact in that we know populations of species have adapted and changed as it is something we can both directly observe today and boasts overwhelming evidence that is has occurred historically throughout time. The mechanism explaining how evolution works is the theoretical portion of the concept, and there are different ways describing this mechanism, which is not completely understood, yet has a vast amount of evidence backing current ideas. Scientists strive to understand the mechanisms (the theory) by which evolution (the fact) has occurred and continues to occur.
History of Evolutionary Theory
“The idea of biological evolution has existed since ancient times, but the modern theory wasn’t established until the 18th and 19th centuries, with scientists such as Jean-Baptiste Lamarck and Charles Darwin. Darwin greatly emphasized the difference between his two main points: establishing the fact of evolution, and proposing the theory of natural selection to explain the mechanism of evolution.” (Futuyma) Though the evolutionary theory was one put forward by Greek philosophers such as Aristotle, and accepted by Leonardo Da Vinci as a possibility, the concept did not gain steam until Charles Darwin published his defining work “On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.”
While Darwin was spending time on the species-rich island of Galapagos, he noticed the rich diversity of species, and hypothesized that life descended from common ancestors. Introduced was Natural Selection, which today is a prevailing concept in biology.
However, Darwin did not have a firm understanding of the entire evolutionary process, particularly the means of how species varied from one generation to the next. “Darwin’s theory, though it succeeded in profoundly shaking scientific opinion regarding the development of life (and indeed resulted in a small social revolution), could not explain several critical components of the evolutionary process. Namely, he was unable to explain the source of variation in traits within a species, and he could not provide a mechanism whereby traits were passed faithfully from one generation to the next.” (Futuyma)
Austrian monk Gregor Mendel’s studies of genetics in the 19th Century, though not appreciated at the time, would fill this need in Darwin’s theory, which has propelled scientific understanding of evolution.
The next revolutions would come with the discovery and understanding of DNA and genetic code. “In the 1940s, following up on Griffith’s experiment, Avery, McCleod and McCarty definitively identified deoxyribonucleic acid (DNA) as the “transforming principle” responsible for transmitting genetic information. In 1953, Francis Crick and James Watson published their famous paper on the structure of DNA, based on the research of Rosalind Franklin. These developments ignited the era of molecular biology and transformed the understanding of evolution into a molecular process: the mutation of segments of DNA.” (Futuyma)
With the discovery of DNA, the picture was almost complete for scientists. In the 1970s, Motoo Kimura formulated the Neutral Theory of Molecular Evolution, firmly establishing the importance of Genetic Drift in the process of evolution.
Soon after, one renowned biologist Stephen Jay Gould put forth the Theory of Punctuated Equilibrium.
Fast-forward 180+ years from Darwin’s time, and the theory has been given a facelift in the light of new discoveries, but the core of the theory remains basically the same as Darwin visualized. “The prevailing formulation of the theory of evolution is the modern synthesis, which brings together Darwin’s theory of evolution by natural selection and Gregor Mendel’s theory of inherited characteristics, now called genes. In the modern synthesis, “evolution” means a change in the frequency of an allele within a gene pool. This change may be caused by a number of different mechanisms: natural selection, genetic drift or changes in population structure (gene flow).” (Futuyma)
Evolution
Here is the definition of evolutionary biology as found in almost any dictionary: “The theory that groups of organisms change with passage of time, mainly as a result of Natural Selection, so that descendants differ morphologically and physiologically from their ancestors.”
“In the context of life science, evolution is a change in the genetic makeup of a population of interbreeding individuals within a species. Since the emergence of modern genetics in the 1940s, evolution has been defined more specifically as a change in the frequency of alleles from one generation to the next. The word “evolution” is often used as a shorthand for the modern theory of evolution of species based upon Charles Darwin’s theory of natural selection, which states that modern species are the products of an extensive process that began over three billion years ago with simple single-celled organisms, and Gregor Mendel’s theory of genetics.” (Futuyma)
It is very important to note that individual organisms do not evolve. Populations evolve.
If one believes the following, then they believe in evolution, whether they know it or not.
1. Each generation of organisms possess slight genetic variations from their parents.
2. That organisms whose traits are the most beneficial survive and reproduce in greater numbers than organisms with less beneficial traits.
3. That the earth has undergone radical and sweeping periods of environmental and ecological change in its history, forcing populations to adapt to their new circumstances.
4. Life on earth dates back to millions of years ago and dinosaurs, other prehistoric creatures, and the fact that 99% of the species to ever exist have gone extinct, are proof of this.
It’s really quite simple.
Artificial Selection
Human beings have been changing creatures for millennia. We have domesticated dairy cows from the dreaded Aurochs, turned nocturnal predators into lap pets with a variety of shapes and sizes, have generated hundreds of breeds of dogs, and have engineered the banana from the unfriendly plantain (despite what Ray “Banana Man” Comfort claimed).
This process is called artificial selection, which is the human-driven selection of desirable traits in the organisms we choose to breed, whether for food or companionship.
The term hybridization is used to describe both wide and narrow crossbreeding. An example of narrow crossbreeding would be crossing black guinea pigs and white guinea pigs, tall with short garden peas, or one flower with another. Examples of wide crossbreeding would be between a radish and a cabbage, rye and wheat, lions and tigers, mules and horses, or a swan and a goose.
That artificial selection can produce such amazing variations in such a small number of generations is a testament to the level of genetic variation that is possible within Earth’s living creatures.
Natural Selection
The “mechanism” of evolution proposed by Charles Darwin is natural selection. Darwin based his explanation on four observations he made about the natural world:
1. In a given generation, species produce more offspring than survive.
2. Individuals differ from one another, whether in appearance or behavior of physiology. After Darwin’s time, scientists have discovered that genes are the inherited factor that makes one different from one another. The environment also causes variation, and this is not disputed, but natural selection is only supposed to work on what is inherited between generations.
3. Resources are limited, and as a result, individuals compete for these resources, hence ‘the survival of the fittest’.
4. Individuals with characteristics that allow them to secure more food, growing space, or more mates leave more offspring in successive generations. Therefore, the ‘more fit’ individuals tend to pass their characteristics on because they better survive the current environmental conditions.
The Hardy–Weinberg principle is a null-hypothesis that states populations will not evolve (e.g. no natural selection/mutation leading to evolution) under certain conditions. It states that if there is random mating, no mutations, no selection, large population size, overlapping generations, random genetic drift, and no gene flow into the population, that it will not evolve. These conditions are never found in nature simultaneously, meaning that evolution eventually and inevitably occurs in populations of organisms.
Since we have already seen that artificial selection produces radical variations, it is not a stretch to understand how natural processes such as competition and the environment can select for certain traits just as humans can.
Genetics
Gregor Mendel was the founder modern genetics studies. He conducted experiments with pea plants, and realized that characteristics of parents were passed on to their offspring through parts of their DNA.
He defined heredity as a gene, through which traits are inherited from generation to generation. Mendel discovered these principles of inheritance during the late 1800s, but his results were forgotten until the about the early 1900s.
Here are the two Mendelian laws:
1. The Law of Segregation: In the formation of reproductive cells, pairs of genes controlling a given characteristic separate from each other and go into different reproductive cells.
2. The Law of Independent Assortment: In the formation of reproductive cells, genes for different characteristics (e.g. stem length and color of a flower) assort independently of each other, and in fertilization, they recombine by chance. (Heinze, p. 67)
DNA: “Deoxyribonucleic acid (DNA) is a nucleic acid which carries genetic instructions for the biological development of all cellular forms of life and many viruses. DNA is sometimes referred to as the molecule of heredity as it is inherited and used to propagate traits. During reproduction, it is replicated and transmitted to offspring.” (Calladine)
Gene: “Genes are material entities that parents pass to offspring during reproduction. These entities encode information essential for the construction and regulation of polypeptides, proteins and other molecules that determine the growth and functioning of the organism.” (Pearson) Genes are small segments of DNA. They occupy a specific position on a strand of DNA called a ‘locus’. Genes contain information about various parts of our body and our traits, such as height, eye color, hair color, and every other variation that makes us unique.
Allele: “An allele is any one of a number of alternative forms of the same gene occupying a given locus (position) on a chromosome. An example is the gene for blossom color in many species of flower – a single gene controls the color of the petals, but there may be several different versions of the gene. One version might result in red petals, while another might result in white petals.” (National Geographic Society) The two types of a single gene are called ‘alleles’. There are two alleles for every trait or characteristic stored in the genes. T and t are the two alleles that control the height of a plant. When organisms have two allele of the same kind, it is known as homozygous and when both are different, it is called heterozygous. The number of times a certain allele is present in a population of species is called allele frequency.
Recessive and Dominant: Alleles are labeled as being either recessive or dominant. Take the two alleles for height, T and t. When a plant is very tall, it has been found out that the T allele is present and the presence of the other allele does not matter at all. The T allele is then considered to be the dominant allele. The t allele’s effect cannot be seen when the T allele is present, making the t allele recessive. Only if both the alleles are t will the plant will be short. So single allele whose effect can be seen, is called the dominant allele. Alleles that can produce an effect only when in pairs are known as recessive alleles. (National Geographic Society)
Phenotypes and Genotypes: The observable characteristics of individuals are called ‘phenotypes’. “The phenotype of an individual organism is either its total physical appearance and constitution, or a specific manifestation of a trait, such as size or eye color, that varies between individuals.” (Brenner) The sound of one’s voice or the shape of one’s nose is a phenotype. The genes carried by an individual, which govern a certain trait, are known as ‘genotypes’. “The genotype is the specific genetic makeup (the specific genome) of an individual, usually in the form of DNA. It codes for the phenotype of that individual.” (MedTerms)
The Gene Pool: The collection of every gene of all of the people in a population is called a gene pool.
Here is a simple summary of genetics:
1. The unit by which traits are inherited is the gene.
2. All individuals have two alleles for each of their characteristics.
3. All individuals have a phenotype (what they look like) and a genotype (what alleles they possesses).
4. Alleles can be either dominant and be seen on the outside or be recessive and not be represented in the individual’s outer appearance.
5. Alleles divide during mating and each reproductive cell carries one allele of each of that parent’s pair of alleles. Each individual thus inherits one from their mother and one from their father.
6. Allele systems assort randomly, meaning whatever alleles one has for one characteristic should not influence what alleles one has for any other characteristic, e.g. eye color has no connection with height.
Mutation
Mutation is the mechanism that works with natural selection to forge new traits in a population and the formation of new species. Mutations are a change in an organism’s genetic code during DNA replication, and there are several different kinds with different effects.
Mutations can be reflected in an organism’s looks and appearance (phenotype) or internal makeup (genotype). Mutations are random, and many individual organisms, including humans, have between 50-100 mutations in their genetic code. (Talk Origins)
Most mutations are neutral, and a small number are either harmful or beneficial, depending upon the circumstances.
Most genes are exceedingly stable and different genes have different rates of mutation. Mutations can occur at any point in the life of an organism. Two members of a pair of genes mutate independently, just as different genes do, and mutations with slight to no visible effect are far more common that those with marked effects. All genes are self-propagating, and are ultra-microscopic in size.
Genetic Drift and Gene Flow
While flipping a coin a hundred times, we’ll probably get a ratio of 50:50 = 1:1, a fifty/fifty ratio of heads to tails. But what if we were to flip it ten times? We might get seven heads and three tails and the ratio may not be 1:1 as frequently. This is what is happens with genetic drift. The heads and tails are the alleles, the coin is the individual, and nature flips the coin.
“Genetic drift is a mechanism of evolution that acts in concert with natural selection to change the characteristics of species over time. It is a stochastic effect that arises from the role of random sampling in the production of offspring. Like selection, it acts on populations, altering the frequency of alleles and the predominance of traits amongst members of a population, and changing the diversity of the group. Drift is observed most strongly in small populations and results in changes that need not be adaptive.” (Avers)
Genetic drift is a random change, either an increase or decrease, in the frequency of an allele.
Suppose a population of 10 people have two alleles for hair color: A and a. We might find many redheads in the parent generation, yet more blondes among their offspring. This sort of variation will either help or become a problem to the species, and natural selection filters which variation will remain, as those with the less helpful hair color (blondes) will die out and those with the more helpful (redheads) will live on. If we have a small population reproducing, we are limiting the available number of coin flips. The ratio between two different features can shift dramatically from one generation to the next in small populations. This shift in frequency is an example of genetic drift.
Genetic drift can begin a trend that results in one feature vanishing completely from the gene pool of small groups, thus decreasing or eliminating variation in that feature within the population. But, since the change is totally undirected and random, the changes of allele frequencies in several different small groups of species are very likely to be different. This is why it is considered a random process and impossible to predict on many levels. (Avers)
Gene flow is the introduction of new genetic material either into or out of a population, which changes the gene pool, and potentially produces the emergence of new traits.
Speciation
A biological species is a population that has become reproductively separate from other populations. Speciation is the process by which this occurs.
Speciation is what many fundamentalists are actually referring to when they say they reject evolution, and it is the most misunderstood concept when debating biology with opponents of evolutionary theory.
There are two modes by which speciation takes place:
Allopatric Speciation: This has to do with species rising due to geographical separation. An example would be if part of a population wandered far away and got stranded, they theoretically would have to adapt to that environment, leading to changes directed by either natural selection or the surrounding environment over time. At any point in time the geographic ranges of the populations could change again. The separated populations may merge together and their individual members mingle together and meet. What happens next depends on how much the two populations have evolved while apart. If they are still basically the same, their members may mate together and the two populations simply fuse into one. But if they have become too different, they will not be able to interbreed and the two populations would then have become two distinct species. (Fickel)
Sympatric Speciation: This is a form of natural selection that leads a population to becoming reproductively different while sharing the same space. When a population of organisms becomes reproductively different, they cannot mate with each other and will thus gradually diverge into two species. The first step is for natural selection to favor the evolution of two forms within the continuous range of the same species. If the force of natural selection is strong enough, two forms could evolve. If the process continues for long enough, the two forms might diverge into different species. If the offspring between individuals of the same form survived better than the offspring of different forms, natural selection would favor a reduction of interbreeding between the two forms. Speciation would then result from this divergence followed by natural selection to reduce interbreeding. (Huber)
Punctuated Equilibrium
Small variations that fit an organism slightly better to its environment are selected and more individuals with more of the helpful trait survive, while others with the less helpful trait die. Most populations evolve very gradually, and variation can be harder to notice over short periods of time.
However, there is a time when evolution dramatically leaps forward. “Punctuated equilibrium is a theory of evolution which states that changes such as speciation can occur relatively quickly, with long periods of little change—equilibria—in between.” (Mayr)
Dr. Stephen Jay Gould and Dr. Niles Eldredge noticed when studying the fossil record that creatures did not always slowly evolve, so they hypothesized that changes can happen far more rapidly.
Punctuated equilibrium states that populations remain stable for long periods of time, evolving little or not at all in periods called “stases.” Small isolated populations evolve rapidly so that speciation takes place over about ten thousand to a million years, a geological instant. Punctuated equilibrium explains how large stable populations can produce new species in that the large population itself does not change, but small isolated ‘pockets’ of the population might. This would result in a branching rather than linear species histories. It also attempts to explain the relative scarcity of transitional forms in paleontology. (Mayr)
Phylogeny
Scientists have classified every known species into these “kingdoms,” and use these classifications:
Kingdom Monera – Prokaryotes (Organisms without a clear nucleus)
Kingdom Protista – Unicellular eukaryotes (Single celled cells with a nucleus)
Kingdom Plantae -Multicellular plants
Kingdom Fungi – Saprophytic and parasitic fungi.
Kingdom Animalia – Multicellular animals.
“According to the theory of common descent, modern living organisms, with all their incredible differences, are the progeny of one single species in the distant past. In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all life. Some of the macroscopic properties that characterize all of life are (1) replication, (2) heritability (characteristics of descendents are correlated with those of ancestors), (3) catalysis, and (4) energy utilization (metabolism). At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree. If every living species descended from an original species that had these four obligate functions, then all living species today should necessarily have these functions (a somewhat trivial conclusion). Most importantly, however, all modern species should have inherited the structures that perform these functions. Thus, a basic prediction of the genealogical relatedness of all life, combined with the constraint of gradualism, is that organisms should be very similar in the particular mechanisms and structures that execute these four basic life processes.” (Theobald)
A phylogeny illustrates the origin and evolution of individual species. It is a major task to determine the ancestral relationships among known species, both living and extinct. Phylogenetics is the practice of classifying organisms within an evolutionary hierarchy and tracing them to their common ancestor. (Maher)
Evolutionary Eras
This is the geological timeline that scientists refer to. All of these are divided by a series of mass extinctions or by the rise of a particular genus. (Talk Origins) This is well understood by scientists from the study of fossil records and geological layering, which both tell a detailed story for the history of the Earth and the life it supports.
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Era/Period/Epoch |
Time |
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Archaeozoic (Archean) era |
5000-1500 |
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Proterozoic era |
1500-545 |
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Paleozoic era |
Cambrian period |
545-505 |
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Ordovician period |
505-438 |
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Silurian period |
438-410 |
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Devonian period |
410-355 |
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Carboniferous (Mississipian/Pennsylvanian) period |
355-290 |
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Permian period |
290-250 |
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Mesozoic era |
Triassic period |
250-205 |
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Jurassic period |
205-135 |
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Cretaceous period |
135-65 |
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Cenozoic era |
Tertiary period |
Paleocene epoch |
65-55 |
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Eocene epoch |
55-38 |
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Oligocene epoch |
38-26 |
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Miocene epoch |
26-6 |
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Pliocene epoch |
6-1.8 |
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Quarternary period |
Pleistocene epoch |
1.8-0.01 |
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(Lower Paleolithic) |
0.50-0.25 |
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(Middle Paleolithic) |
0.25-0.06 |
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(Upper Paleolithic) |
0.06-0.01 |
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Holocene epoch |
0.01-0 |
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Fossil Records
The layering of strata is an important tool that naturally divides fossils into the era in which they lived. One of the great proving grounds for natural selection are worldwide catastrophes. These not only explain the abrupt fossilization and layering of fossils into the strata, but it also is used to explain the mass extinctions of various creatures throughout time. The evolutionary eras are divided by mass extinctions and planetary catastrophes.
The fact that there are fossils at all is proof of these catastrophes, since most creatures don’t fossilize when they die, and it usually takes a sudden disaster such as a flood or volcanic eruption to bury and preserve them.
Strata is neatly layered into various fossil groups. From the lowest (oldest) layers we see very small, simple fossilized organisms, and the higher we go, we see more and more complex and increasingly large fossils. To scientists, this is a snapshot into the past, and that evolution has been frozen for all to see. Whether one traces from the topmost, current layers, to the lowest, oldest layers, or vice-versa, it remains that this observation is sound, that being “simple” fossils are shown to be older, and more complex fossils are younger.
Embryology
Many human embryos have tails in their early and middle stages of development. A minority of babies actually retain this tail at birth and doctors surgically remove it shortly thereafter, and some have reached lengths of 9 to 13 inches long. And of course, all humans have a ‘tailbone’ that is located exactly where the tail of an animal would attach. (Bakker)
Comparative embryology shows stark similarities between the embryos of different species in the early stages, demonstrating common ancestry.
The study of Ontogeny shows features in the embryos of a species can contain vestiges left over from an evolutionary ancestor that do not manifest themselves when the baby is born. For example:
mammalian ear bones and reptile jaws
pharyngeal pouches and branchial arches
snake and whale embryos with legs
embryonic human tail
marsupial eggshell and caruncle similar to those of birds and reptiles
Comparative Anatomy
A common way for scientists to determine the relationship between organisms is to compare them, either genetically or superficially.
Scientists compare an organism’s morphology (physical appearance) to that of others.
Homology is the practice of comparing organs between organisms to derive ancestry.
Vestigial organs are organs in the body of a creature that are left-over from evolutionary development. Scientists see an organ that appears to be without use or function, and assume that it is merely left over from evolutionary processes. Examples of known organs or features that are considered vestiges include living whales that have been found with hindlimbs, and newborn human babies born with tails.
Observation
There have been many observed instances of evolution in action.
There is a particular moth that is typically whitish with black spots, which provides an effective camouflage for the moths as they rest on certain Birch Trees. These moths however, can be found in a wide range of pigmentation from very black to very white, and almost every shade in between. An English study found that when the whites upon which the moth rested became dark from industrial pollution, birds were able to eat more of the lighter moths, as they could not camouflage as well anymore, and completely missed the darker ones.
Unsurprisingly, the population of darker moths increased drastically, while the population of lighter moths sharply decreased. However, it was observed that after the cities cleaned up the air, the trees become lighter and the lighter moths again dominated. This Natural Selection in action and proof of one of Darwin’s primary theories. The problem with this though is that there is no evolution occurring and that it is being used as proof of the theory. At the start of the study there were both light and dark moths, and at the end of the study there were both light and dark moths. While no new trait has been acquired and there has been no increase in genetic complexity, and the only difference has been a shift in the color distribution of the Peppered Moth population, this is not what the study was aiming to prove. Those who object to the theory complain that this should not be used as proof of evolution. However, it is proof of Natural Selection, which is a part of the theory.
Through selective breeding, experiments with fruit flies have found that they can breed generations of flies with messed-up biological clocks and sleep cycles that are caused by mutations. The same has been done with the eye color fruit flies. Selective breeding experiments have shown that mutations can be passed through generations.
Sickle-celled anemia is caused by an inherited defect in the instructions that code for the production of hemoglobin, the oxygen-carrying pigment in red blood cells. One will only develop the full-blown serious disease if parents had the defective gene. If one inherits the defect from only one parent, the healthy gene from the other one will largely enable one to escape the effects of this serious condition. However, this means one is capable of transmitting the defective gene to their offspring, and such carriers are less likely to develop the often-fatal disease malaria. Carriers of sickle-cell disease who do not suffer it are far more common in those areas of the world that are high-risk malaria areas, such as Africa.
DNA Evidence
Creationists argue that fossils only reveal bone structure, which is true, but that somehow isn’t enough for them. Well, they’re in luck, because DNA evidence is right there in a pinch to erase all doubt about common ancestry between humans and primates.
What about the simple genetic fact that apes have 48 chromosomes and man only 46? This seems like a significant difference, however evolution predicts that this can be explained by instead of 2 chromosomes disappearing, they instead fused into one. And this is exactly what we find, right at chromosome 2. Creationists ignorantly try to say that this makes a huge difference, however what they don’t seem to know or want to acknowledge is that 1 human in every 1300 actually has a fused chromosomes 13 and 14, to no visible difference to the rest of humanity. Regardless of whether the chromosome is fused or not, the same genetic coding is present.
That humans and apes share a common ancestry is easily provable through DNA, and not simply because we share 98.5% of our genome with chimpanzees. Rather, it can be proved by markers in DNA called endogenous retroviruses, (ERVs).
Retroviruses are viruses that reverse-transcribe their RNA into DNA for integration into the host’s genome. Most retroviruses (such as HIV-1) infect somatic cells, but some can also infect germline cells (cells that make eggs and sperm) and once they have done so and have been transmitted to the next generation, they are termed “endogenous.”
ERVs are retroviruses derived from ancient viral infections of germ cells in humans, mammals and other vertebrates; as such their proviruses are passed on to the next generation and now remain in the genome. Endogenous retroviruses can persist in the genome of their host for long periods. However, they are generally only infectious for a short time after integration as they acquire ‘knockout’ mutations during host DNA replication. They can also be partially excised from the genome by a process known as recombinational deletion. They play a key role in evolution.
How this applies to primate/human genetic relations is simple. If we take a chimp’s DNA and line it up with a human’s, it looks remarkably similar. The chromosomes look precisely the same. The genes line up in the exact same order. And it’s not just the functional bits that line up perfectly. On the short arm of chromosome 10, we find something fascinating: the relic of a viral infection, an ERV. It’s important to note that the virus’ DNA inserts itself randomly into the host chromosome, and if it infects one of the germ cells involved in reproduction, it gets passed on to ALL future generations.
The interesting thing is, chimps and humans have the same ERV in the same location on chromosome 10. The chances of a pair of ERVs inserting themselves in the same location is 3 billion to 1. On the short arm of chromosome 1, we find yet another remnant of a viral infection, which we also have in common with chimpanzees. The odds of 2 pairs lining up is 4,500,000,000,000,000,000 to 1. And then on chromosome 19, we find a third identical ERV. In all, we share 16 identical ERV infections in our DNA. And those are just K CLASS VIRAL INFECTIONS. There are actually 98,000 ERVs found in the human genome, the vast majority of which we share with primates.
The odds of this are mindbogglingly small. Creationists try to argue that ERVs are not the remnants of viral infections, which is a lie, because they look exactly like the genomes of retroviruses, and we ACTUALLY OBSERVE ERVs forming after a retrovirus infects a cell.
The only way this makes any sense is if we share a common ancestor with chimpanzees, as science predicts, therefore increasing the odds of this happening to 1. And because of this, we can also trace the exact point where ape and human populations diverged into their separate branches.
For the next piece of genetic evidence, somewhere in our genome is a very curious stretch of DNA. Located on the short arm of chromosome 8 we find 152 unassuming nucleotides, which matches the gene for exon 10 of the GULO perfectly, which is the gene responsible for vitamin C biosynthesis in animals. So what? Well, humans don’t actually have this protein. It’s why we need to consume vitamin C lest we get diseases such as scurvy. We also don’t produce any mRNA for this protein, yet the genetic code exists anyway, which is completely nonfunctional. We know it’s nonfunctional because this specific code is rife with mutations and other information that would be harmful to us if active.
So why is it there? Our only options are that it appeared spontaneously or that it evolved from a previously functional gene. The chances of a 152 nucleotide stretch of DNA that’s perfectly identical to another found in other creatures is astronomical. Yet the most interesting part is that other primates also have this exact same stretch of non-functional genetic coding, and also do not posses the trait of vitamin C biosynthesis. The chances of 4 or more species having genomes with this exact string of nonfunctional coding is nigh impossible.
Fundamentalists have no counter for this, other than to jump up and down screaming that the genetic code is functional, despite numerous studies proving otherwise.
Genetic piece of evidence number three of many can be explained as follows: protein sequence is produced through the translation of a non-overlapping degenerate triplet code. These mutations will not affect the protein and therefore have no effect on the organism. The complicate here however is that codon bias can affect the rate of translation and impact the organism. Humans though have one special amino acid coded by
GAA
GAG
which shows no bias, therefore switching codons has no effect. So what does this apparent gibberish mean? Evolution predicts that closely related species should glutamic acids the exact same way because there has not been enough time for the populations to diverge. We find exactly that since primates have the exact same coding. All 12 glutamic acid positions match with the same coding as above, the chances of which are nearly impossible.
How Whales Work
Scientists, on the whole, were unable to explain how the whale, which is a mammal, crawled back into the sea without leaving any believable fossil evidence of intermediate forms. Since the days when the whale was the biggest problem for scientists, they have made some significant discoveries.
Michael Behe spent pages and pages in “Darwin’s Black Box” ripping evolutionary scientists on whale evolution. What happened shortly thereafter, however, was a blitz of fossils revealing the evolutionary history of whales:
Sinonyx: A wolf-sized mammal from the late Paleocene, about 60 million years ago. The characteristics that link Sinonyx to the whales include an elongated muzzle, an enlarged jugular foramen, and a short cranium. The tooth count was 44, typical of mammals of the era. The teeth were differentiated, as are the teeth of today’s mammals. The molars were very narrow shearing teeth, especially in the lower jaw, but possessed multiple cusps. The elongation of the muzzle is often associated with all fish, hunting whales, and dolphins. (Talk Origins)
Pakicetus: 52 million years ago. Known only from fragmentary skull remains. The upper and lower molars are still similar to those of Sinonyx, but the premolars have become simple triangular teeth. The teeth of later whales show even more simplification into simple serrated triangles, like those of carnivorous sharks, indicating that Pakicetus’ teeth were adapted to hunting fish. (Talk Origins) Paleontologists believe that Pakicetus was a quadrupedal mammal.
Ambulocetus: Found in the same area that Pakicetus was in Pakistan. Called “the walking whale that swims”. Dated from 50 million years ago. Had functional legs and a skeleton that still allowed some degree of walking on dry land, though not very well. Described as an amphibious, sealion-sized fish eater that was not yet totally disconnected from the terrestrial life of its ancestors. (Talk Origins)
Rodhocetus: In the middle Eocene, 46 million years ago, Rodhocetus took all of these changes even further, yet still retained a number of terrestrial features. Supposedly, it had a powerful tail for swimming and was the first to show blowhole evolution. (Talk Origins)
Basilosaurus: 35-45 million years ago. Basilosaurus was a long, thin, serpentine animal that was originally thought to have been the remains of a sea serpent. Scientists say its extreme body length appears to be due to a feature unique among whales. (Talk Origins)
Dorudon: 40 million years ago. It was most like modern whales. Lacked the elongated vertebrae of Basilosaurus and was much smaller. Dorudon’s teeth were similar to Basilosaurus’. But it did not have the ability of echolocation. (Talk Origins)
One of the most self-evident proofs of whales and dolphins have a terrestrial origin is to simply watch them swim. All other creatures, such as fish, who are native to the waters with fins and all, swim by moving from side to side. However whales and dolphins, being mammals, swim up and down, like any land-dwelling mammal would while swimming with their legs, which neither dolphins or whales have. If these were always sea-dwelling creatures, there would be absolutely no reason for them to swim as if they had legs, and even less reason for them to not be able to breath underwater since just about every else in the oceans can. Also, these creatures are smart, which is something most mammals have going for them, and something that most aquatic life simply doesn’t. Fish and other purely native ocean-dwellers are really, really dumb. Go to a large aquarium sometime, preferably somewhere with a dolphin or killer whale show, and it’s pretty easy to see these creatures’ evolutionary roots simply in how they behave.
Human Evolution
“One of the most celebrated examples of transitional fossils is our collection of fossil hominids. Based upon the consensus of numerous phylogenetic analyses, Pan troglodytes (the chimpanzee) is the closest living relative of humans. Thus, we expect that organisms lived in the past which were intermediate in morphology between humans and chimpanzees. Over the past century, many spectacular paleontological finds have identified such transitional hominid fossils.” (Theobald)
(A) Pan troglodytes, chimpanzee, modern
(B) Australopithecus africanus, STS 5, 2.6 My
(C) Australopithecus africanus, STS 71, 2.5 My
(D) Homo habilis, KNM-ER 1813, 1.9 My
(E) Homo habilis, OH24, 1.8 My
(F) Homo rudolfensis, KNM-ER 1470, 1.8 My
(G) Homo erectus, Dmanisi cranium D2700, 1.75 My
(H) Homo ergaster (early H. erectus), KNM-ER 3733, 1.75 My
(I) Homo heidelbergensis, “Rhodesia man,” 300,000 – 125,000 y
(J) Homo sapiens neanderthalensis, La Ferrassie 1, 70,000 y
(K) Homo sapiens neanderthalensis, La Chappelle-aux-Saints, 60,000 y
(L) Homo sapiens neanderthalensis, Le Moustier, 45,000 y
(M) Homo sapiens sapiens, Cro-Magnon I, 30,000 y
(N) Homo sapiens sapiens, modern
List of human evolutionary fossils.
Ida: The most recent fossil find related to primate evolution was just as new as 2009. Also called “Darwinius,” Ida is a fossil found in 1983 in the Messle pit southeast of Frankfurt, Germany. The fossil was not reassembled until 2007. Ida lived 47 million years ago and appears to have been the close relative of the modern day lemur. What makes this so exciting is that the fossil is 95% complete, missing only its left rear leg. Remains of her soft tissue and fur are also present, also with the remnants of her last meal of fruits and leaves. It’s 58 cm long, about the size of a long-tailed cat. The fascinating features of Ida are opposable thumbs and nails, similar to those of a humans, instead of claws. Unlike lemurs, she does not possess a grooming claw on the foot, or a ‘tooth comb’, a fused row of teeth, in her mouth. It’s also important to note that modern lemurs only exist in Madagascar today, far away from Germany. Ida possess traits that modern lemurs do not have and vise-versa. Ida is considered a close cousin of humans rather than a direct ancestor. This is definitive fossil proof of primate evolution.
Dispelling Creationist Misconceptions
Some common misconceptions about evolutionary theory need to be dealt with. These are due either to distortions by skeptics, or just pure mis-education in the school systems and the media.
1. The first and most common misconception is that humans are “made-over monkeys”: Despite what many think, this is a widespread misconception. Humans and chimpanzees merely had a common ancestor.
2. Evolution is not to be confused with Social Darwinism, a societal view restricted to the realm of philosophy.
3. Many religious people, including some scientists, view belief in God and evolution as compatible, despite fundamentalist claims.
4.”What good is half a wing?’ This constant creationist argument demonstrates pure ignorance of biology, as all changes would be advantageous within the confines of the evolutionary theory, and there are no “incomplete organisms” as every species is complete for its generation. If a reptile would have grown just half a wing the species would have died out, as they were not fit enough to survive.
5. The study of stellar evolution, e.g. the Big Bang Theory, planet formation, and the like are separate from the study of evolutionary biology, which is confined to the sphere that is our planet and the life therein.
6. Man is not the goal of the evolutionary process. This is ridiculous and only ignorant fundamentalists believe this.
7. Fundamentalists say that evolution has never been observed. This is not true, as has been demonstrated.
8. An often-cited argument against evolution is the Second Law of Thermodynamics, which states that all things move towards entropy, or breaking down, while with the theory of evolution, life continues to grow more complex. However, second law only applies to closed systems, not an open biosphere such as the Earth, where the sun is supplying a never-ending amount of energy to replenish the system.
9. In nearly 200 years of evolutionary science, there have been many false claims made by people trying to find the “missing link,” and creationists view this as a systemic corruption of science. There have been some people who have grafted parts of monkey skulls to the skull of a man in an effort to fake a hybrid monkey-man. Though some of these claims of falsified evidence may be true, most scientific discoveries are rigorously vetted by the peer review process, and in this day and age, it is extremely difficult for the same kinds of hoaxes that took place 200 years ago to skirt by unnoticed.
10. Creationists also argue that apes have a ‘baculum’, a hard bone in the penis, man does not, and given the simple fact that this had to work right the first time in order to propagate the race, how could such a radical change have ever occurred? Most mammals have a baculum, humans being a notable exception on a short list. Great apes have a very small bone in the penis, measuring only three quarters of an inch in size, the rest of the organ completely resembling a humans. Therefore the gradual disappearance of this bone could never have affected the propogation of the species in any way at all, dismantling this
11. Creationists constantly claim “THERE ARE NO TRANSITIONAL FORMS.” Technically, every creature is a transitional form, and the search for the “missing link” is a misnomer. In reality, there are a lot of creatures they may never find full fossilized lineages for, due to the simple fact that most living things don’t fossilize when they die. To ask for every single possible transitional form in an evolutionary tree is being unfair and is asking for something impossible to find. Many evolutionary trees may be imperfect and fragmented. A lack of examples of the theory however does not void the already established processes and rules. We know and have proven enough of the Evolutionary Theory to show that it happens, even if we don’t always know exactly how its manifested itself every step of the way.
12. “BIRDS COULD NEVER HAVE COME FROM DINOSAURS,” creationists claim. Velociraptors, one of Hollywood’s favorite dinosaurs, is now know to have had feathers. In September 2007, researchers found quill knobs on the forearm of a Velociraptor found in Mongolia. These bumps on bird wing bones show where feathers anchor, and their presence on Velociraptor indicate it too had feathers. “A lack of quill knobs does not necessarily mean that a dinosaur did not have feathers. Finding quill knobs on Velociraptor, though, means that it definitely had feathers. This is something we’d long suspected, but no one had been able to prove.” (Turner)
13. The Coelocanth was a fish long thought to be extinct and touted as the first fish to rise from the water and walk on land. The fish was thought to have died out 400,000,000 years ago, that is, until it was caught off the coast of Africa, alive and virtually unchanged from its fossilized ancestors, save for its size, which is slightly larger than its ancestors. Creationists cite this as proof against the evolutionary theory, as there has been no evolutionary change in the fish, and that it is in fact a very complex fish, as it uses electromagnetic pulses to search for food. Scientists however, counter that due to the fact that it lives deep in the ocean, there was very little competition or other external factors influencing its evolution. Without natural selection to kill-off and select for certain traits, populations do not evolve. In fact, there are many creatures that have shown no signs of evolution for even the millions of years: the nautilus, horseshoe crabs, king crabs, mollusks, sharks, and crocodiles. These creatures are perfectly suited to their environments, so there are no pressures forcing their populations to evolve.
14. Creationists like to attack evolution with arguments from probability, basically claim that the “chances of life arising on Earth and producing complex organisms are next to zero.” Sir Fred Hoyle, a British mathematician and astronomer, was quoted in ‘Nature’ magazine, November 12, 1981, as saying “The chance that higher life forms might have emerged in this way [evolution] is comparable with the chance that a tornado sweeping through a junk-yard might assemble a Boeing 747 from the materials therein.” (Heinze) Creationists have taken the previous quote and beat it to death for decades. The probability argument however does not hurt evolution at all, as scientists argue that it only had to happen once, and that life is likely to occur on any planet with the proper ecological conditions.
15. Creationists claim that the sun’s diameter is supposedly shrinking at the rate of five feet per hour. At this rate, life could not have existed on the earth 100,000 years ago. This would not only aids in the dispelling of the evolutionary theory, but it also lends credence to the creationist claims that the earth is merely 6000-7000 years old. Scientists, however, say that the sun is not shrinking at any constant rate and that preliminary readings were incorrect.
16. Creationists claim the earth’s magnetic field is decaying rapidly, at a constant, if not decreasing rate. At this rate, 8,000 years ago the earth’s magnetism would have equaled that of a highly magnetic star, which is a highly unlikely occurrence. Also, if the electric currents in the planet’s core are responsible for the earth’s magnetism, the heat generated by these currents 20,000 years ago would have dissolved the earth. Scientists say this is complete nonsense.
17. Another creationist argument brings us to the moon. Meteoritic dust falls on the earth continuously, adding up to thousands, if not millions, of tons of dust per year. Realizing this, and knowing that the moon also had meteoritic dust piling up for what they thought was millions of years, NASA scientists were worried that the first lunar ship landing on the moon would sink into the many feet of dust which should have been accumulated. However, only about one-eighth of an inch of dust was found, indicating what creationists interpret to be a rather young moon. Meteoritic material contributes nickel to the oceans. Taking the amount of nickel in the oceans and the supply from meteoritic dust could yield an approximate after of the earth. (Heinze, p. 39) Good luck measuring that however. Matter transitions into other forms all the time. Nickle can change into other substances over time, so it’s nigh impossible to use nickel levels in the ocean to determine how long the moon has been there.
18. Physicist Robert Gentry has reported isolated radio halos of polonuim-214 in crystalline granite. The half-life of this element is a mere 0.000164 seconds. To record the existence of this element in such short time span, the granite must be in crystalline state instantaneously, and this is against evolutionary estimates of 300 million years or so for granite to form. (Gentry) Scientists have no idea what he’s talking about.
19. Another common creationist claim is that measurements of the sediment deposited as a result of Nile’s flooding each year leads to the conclusion of an earth under 30,000 years old. Needless to say, if this adds up, it would make the earth far too young for evolution to have occured as currently cited. Unfortunately, it’s tough to prove that the Nile River has always existed in its current form and configuration.
20. A popular argument against evolution is that the human eye is far “too complex” to have ever evolved from anything even remotely related to a primate. Michael Behe is famous for making and demonstrating this argument. It is true that besides the human brain, the human eye is one of the most complex organs known to exist. However, a recent hypothesis has at last been put forward to try and answer this challenge. According to a news bulletin from the European Molecular Biology Laboratory, the necessary complex cells for the molecular development of the human eye came from the brain. “It is not surprising that cells of human eyes come from the brain. We still have light-sensitive cells in our brains today which detect light and influence our daily rhythms of activity,” explains Wittbrodt. “Quite possibly, the human eye has originated from light-sensitive cells in the brain. Only later in evolution would such brain cells have relocated into an eye and gained the potential to confer vision.” (EMBL) They apparently have only demonstrated this in a marine worm however, showing that the possibility existed for them.
21. Dinosaur researchers across the world were stunned to silence by the announcement that in March of 2005, a 70-million-year-old T-Rex fossilized leg bone had yielded unfossilized soft tissue, blood vessels and blood cells, something long thought to have been impossible. For years, paleontologists have held that organic materials such as animal remains could not be preserved beyond 100,000 years. However, despite creationist finger-pointing, this ‘soft tissue’ was trapped within the bone and had to be extensively re-hydrated to even identify what it was, and any traces of DNA disappeared long ago. While this means we know less about fossilization than previously thought, it doesn’t disprove the age of the dinosaurs.
22. Creationists claim many of the dating methods used for determining the age of fossils are “unreliable.” Carbon14 dating is usually sound within a few hundred years span of time, but there are exceptions to this. For example, a living mollusk was dated using the carbon14 method, and the readings said it had been dead for 3000 years. Dating methods such as uranium-lead, potassium-argon, and rubidium-strontium are used in place of Carbon14 for older rocks. These methods are based on chemical change (uranium to lead, etc.) where the parent material (i.e. uranium), is converted to the daughter material (i.e. lead) at a known rate, called a half-life.
Wizards of ID
The current scientific firestorm is centered around the battle between science and Intelligent Design (ID).
ID states that current life on earth is “far too complex” to have evolved within the given timetable, and therefore scientifically requires “divine intelligence” to exist. The basic premise is that since “life cannot come from non-life,” and that DNA is “far too vastly complex” to have evolved in the relatively brief period of the Cambrian Explosion, the “only explanation” is that there must be an intelligent designer behind it all.
This is actually gaining some notable support with the general public, at the same time as receiving a lot of criticism from actual scientists. Fundamentalists see intolerance and a conspiracy within the scientific community to lock-out competing ideas.
However, ID is just the newest face of creationism, and it is rejected on that basis. The same people who were pushing Young Earth Creationism to be taught in schools are pushing ID today. The fundamental concept of ID is not provable or demonstrable in a laboratory, which is hilarious considering that Michael Behe, one of ID’s biggest pushers, bases his most scathing reviews of evolutionary theory on the number of things he says cannot be demonstrated under lab conditions.
To Michael Behe, “irreducible complexity” refers to microscopic systems, such as genes and cells, which are “too complex” to have formed by the processes described by Darwinian evolution. He uses the example of a mousetrap, which could not function without each one of its parts already being present and working properly. He claims that natural selection can only make use of systems that are already complete and working, therefore the existence of these “irreducibly complex” biological systems is a “powerful challenge” to evolution, because to remove one element from systems such as cells, the entire organism could not function.
Behe uses the example of bacteria, which has a flagella it uses as an “outboard motor” for self-propulsion, which is attached by a universal joint and held in place by proteins. Dozens of different protein types are necessary to allow the flagellum to function, and Behe argues that the absence of any of the parts involved results in the inability of the cell to even built such a mechanism much less use it. He argues that this is evidence of these being “molecular machines”, and since their evolution, in his mind, cannot be adequately explained, they therefore must have their origin with an intelligent designer.
Ken Miller uses Behe’s own mousetrap analogy against him, and he points out that removing two of its parts, such as the catch and the metal bar, may cause the device to lose its definition as a proper mousetrap, but we do suddenly have a three-part machine that could act is a clip for paper or a tie. Taking away the spring gives us a keychain, and the catch could be used as a fishhook and the base as a paperweight. Miller points out that even bits of pieces of Behe’s “irreducibly complex machines” may still have useful functions, even if they do not presently form a mousetrap. This applies to biological organisms as well, rendering Behe’s argument moot.
Regarding Behe’s biological examples, when it comes to bacteria, the group of proteins from the flagellum is used to inject poisons into other cells in absence of the “rest of the machine”. Small parts alone make take on different uses but they are nonetheless functional and can be favored by natural selection. Regarding the blood-clotting example from Behe’s essay, Miller points out that the proteins responsible for clotting blood are actually just modified versions of digestive proteins, and he points out that the work of Russell Doolittle has demonstrated how evolution “retargeted” these proteins and modified them to produce blood-clotting systems in vertebrates.
