Evolution: A Basic Primer
(Part I)


DNA and Evolution (Part II)


Was Darwin Wrong?

Poem-Evolution the Other Side

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This page was last updated 07/16/09

Definition of Evolution:

Possibly most of the controversy that arises in relation to evolution is due to misunderstandings over the terms used.  Therefore, it is probably best to define some of the relevant terms.  Evolution refers to a change in a population over time.  A population is a group of organisms from one species that interbreed and live in the same place at the same time.  For example, a group of people living in the United States right now would be one population and a group of people living in China right now would be another population.  Evolution would refer to changes that occur in the population of people that live in the United States over time.  It is common knowledge that the average height of people in the United States has increased since Colonial days.  It is also common knowledge that the average life span has increased in the United States since Colonial days.  Increases in height and life span would be examples of evolution in the United States population. 

A species is a group of organisms that can interbreed and produce fertile offspring in nature.  The offspring have to be able to reproduce in order to be considered a species.  The breeding of a horse and a donkey creates a mule.  However, mules are sterile and so are not fertile offspring.  Therefore, horses and donkeys are different species.  Some other species are also able to reproduce in a lab setting and produce offspring.  However, in nature theses species would never reproduce due to different geographical location or distinct mating behavior.  For example, there are a lot of different species of fireflies that will only mate with their own species in nature.  Fireflies recognize their own species by the pattern of light flashes during the mating ritual.  Each species has a distinct innate flashing pattern that both the male and female fireflies recognize.  While scientists may be able to induce different species of fireflies to mate in a lab setting the fact that they will not do so in nature still defines them as separate species. 

Speciation is the process of evolution of new species that occurs when members of similar populations no longer interbreed to produce fertile offspring.  It is over this process that most of the controversy arises.  Very few people, if any, disagree that populations do indeed change over time.  The disagreement arises over whether the changes are enough to create new species or account for the diversity of species that exist now or are proven to have existed during earlier times on Earth.  Before speciation can be fully discussed, a few other terms also have to be defined. 

Natural Selection

While visiting the Galapagos Islands, Charles Darwin began noticing that on each of the vastly different islands there were similar animals that varied just a little bit.  He also noticed that the variation helped the animals obtain the food sources specific to a particular island.  After returning to England, Darwin wrote his ideas down in his book Origin of the Species.  Darwin's ideas have since been accepted as the Theory of Natural Selection.  (Note: a theory is an explanation for natural phenomenon based on evidence)

The Theory of Natural Selection has five principles:

The first principle is that there is variation in offspring. 

The second principle is that more offspring are produced than can survive based on available resources. 

The third principle is that competition arises over the limited amount of resources. 

The fourth principle is that those with variations that help them out-compete others to obtain those limited resources will survive and be able to reproduce passing on that favorable variation. 

The fifth principle is that overtime the favorable variation will be seen in more individuals in that population. Generally variations that increase an organism's chance of survival are called adaptations. Also, variations or characteristics that are inherited are called traits.

An example of how natural selection works can be seen clearly in the finches on Galapagos Islands. Each of the Galapagos Islands, off the coast of Ecuador, has its own unique terrain.  Some islands are lush in vegetation and some are rocky with very little vegetation.  Due to the different vegetation on each island, the food available to the finches varies on each island.  As the finches migrated from South America, they landed on the Galapagos Islands.  When the finches reached the first island, those with variations in their beaks that allowed them to obtain and eat the food sources available on that island thrived enough to be able to reproduce and pass on that adaptation.  The finches that did not possess the right kind of beaks to obtain and eat the food either left the island or died.  Therefore, their traits were not passed on to future generations of finches on that island.  On each successive island in the Galapagos, the same process took place.  Finches arrived, those with traits that helped them survive on that island, thrived and stayed to pass on their traits to future generations of finches.  By the time Darwin arrived at the Galapagos Islands, this process had already taken place accounting for the variation in finch beaks he observed on different islands.  

Obtaining Variations
During Darwin's time,
Gregor Mendel was also just beginning to work out the principles behind genetics or how traits are inherited.  Using pea plants, Mendel worked out how traits are passed on to offspring.  Mendel found that for every trait there are two alleles that determine how each trait will be expressed.  Mendel also worked out that during gamete formation the alleles are separated and then recombined during fertilization.  Mendel also worked out that the assortment of alleles into the gametes occurs randomly providing for variation in the offspring.         

Neither Darwin nor Mendel had any idea that DNA was the mechanism controlling how traits were passed down to offspring.  Since we now know that changes in DNA is responsible for variation in traits, we need to first understand the structure and function of DNA. 

Structure of DNA

Deoxyribonucleic acid, DNA, is an organic molecule found in every living cell.

In prokaryotic bacteria cells the DNA floats freely in the cytoplasm.  In eukaryotic cells, cells with a nucleus, DNA is bound within the nucleus.  DNA can also be found within the mitochondria but the function of this DNA is to control production of proteins related only to the mitochondria function.  Since we are more concerned here with how traits are inherited, we will concentrate on the DNA in the nucleus of eukaryotic cells or free-floating in prokaryotic cells. 

Deoxyribonucleic acid, DNA, is a complex organic molecule made up of smaller subunits called nucleotides.  Each nucleotide is made up of a phosphate group, a sugar group, and a nitrogen base group.  In the case of DNA, the sugar group is called deoxyribose.  The nitrogen bases in DNA can be one of four different bases: adenine,
thymine, cytosine, guanine DNA Nucleotides

The next model has the same atomic positions and balls colored by element, but now the sticks convey other information: the backbones are red and blue, and the bases are purple (Adenine), green (Thymine), yellow (Guanine), and cyan (Cytosine).

Each DNA molecule consists of two twisted strands of nucleotides that resemble a twisted ladder.

The sugar and phosphate groups from one nucleotide bind with sugar and phosphate groups from adjacent nucleotides to form the sides of the ladder.

The nitrogen bases on each nucleotide bind with complementary nitrogen bases on the opposite strand of nucleotides.  Adenine always binds with thymine and cytosine always binds with guanine.  When the DNA strands are not in use, they coil up like a spring forming a structure that is referred to as a Double Helix.

Function of DNA

DNA's function is to control the production of proteins that a cell needs in order to survive and carry out the function of the individual cell.  The order in which the nitrogen bases are found on each DNA strand determines what proteins will be produced by the cell.  The sequences of nitrogen bases on a DNA strand is often referred to as a code and is expressed by the capitalized form of the first letter of the nitrogen base.  For example, a sequence on nucleotides containing adenine, thymine, cytosine, guanine, adenine, cytosine, thymine would be expressed

In order to make proteins, the code on a segment of DNA is copied in the nucleus and taken to a ribosome in the cytoplasm of a cell.  The ribosome then uses the code to assemble a protein. 

Production of Proteins

As mentioned earlier, the function of DNA is to control the production of protein in a cell.  DNA does not actually make the proteins. All DNA does is carry the code for the production of each protein. Other types of nucleic acids use this code to assemble the proteins. 

There are three other types of nucleic acids: Messenger RNA (mRNA); Ribosomal RNA (rRNA); and Transfer (tRNA).  These three other types of nucleic acids are grouped together as ribonucleic acids.  Ribonucleic acids differ from deoxyribonucleic acid in three ways.  Instead of two strands of nucleotides, RNA consists of only one strand of nucleotides.  Instead of deoxyribose sugar, RNA contains ribose sugar.  Finally, instead of thymine, RNA contains Uracil. The other three nitrogen bases adenine, cytosine, and guanine are found in both DNA and RNA. Cytosine and guanine remain as complementary bases. However, Adenine now complements uracil. 
The production or proteins begins in the nucleus where the DNA molecule is located.  When a cell needs a specific type of protein a chemical signal is sent to the nucleus.  This chemical signal stimulates an enzyme called RNA polymerase to locate the sequence of nitrogen bases on the DNA strand that carries the code for that particular protein.  The segment of DNA that carries the code for the production of a particular protein is called a gene.  The enzyme then breaks the bonds between the nitrogen bases on each of the two strands of nucleotides on the specified gene.  Using one strand of the exposed DNA segment, the enzyme pairs up complementary nucleotides and binds them together forming a single stranded mRNA molecule.  For example if the gene contains  on one strand, the enzyme will bind a UAAGCSU on a mRNA molecule.  The mRNA then leaves the nucleus and travels to a ribosome out in the cytoplasm of the cell.

A ribosome is an organelle found in all cells. Ribosomes are made up to two units. Each unit contains an rRNA molecule. When the mRNA reaches the ribosome, the rRNA begin to read the code on the mRNA.  The code on the mRNA is read three nitrogen bases, referred to as a codon, at a time.  As rRNA reads a codon, a signal is sent to a tRNA in the cytoplasm that contains a complementary three base sequence, referred to as an anticodon, to the codon on the mRNA. The tRNA then picks up a specific amino acid and brings it to the ribosome. Upon arrival at the ribosome, the tRNA with its attached amino acid is placed on the mRNA. As subsequent tRNA molecules, with attached amino acids, arrive at the ribosome, the amino acids are joined together into a chain and the empty tRNA molecules are released.  When the rRNA reads a stop codon, the chain of amino acids, or protein, is released and sent to the Golgi Apparatus where it is processed for use by the cell. The entire protein assembly process occurs very quickly, almost instantaneously, with numerous proteins being assembled at the same time by numerous ribosomes.    

Its All About Proteins

Proteins are organic molecules that perform countless functions in the cell.  Each protein performs a different function.  Enzymes are special proteins that speed up reactions in a cell without being changed by a cell. They are reusable and without them a cell would not be able to perform cellular activities fast enough to survive.  Other proteins determine our traits such as the protein keratin that gives our hair its structure.  The proteins actin and myosin allow our muscles to move.  The protein melanin gives our skin its color. The protein hemoglobin allows our red blood cells to carry oxygen from our lungs to our cells and carbon dioxide from our cells to out lungs.  Everything about us and everything we do is determined by our proteins.  So how does all of this relate to evolution?

A mutation is referred to as any change in the DNA sequence that contains the codes for the production of one protein.  When there is a change in the DNA sequence of nitrogen bases, such as from ATTCGAT to TATCGAT, a mutation has occurred. When that gene is copied onto a mRNA molecule, the codon for the first amino acid will be different than it should have been before the mutation. Since the codon is different, the amino acid assembled onto the resulting protein will be different. Since the amino acid is different, the resulting protein will be different. Sometime the change in the protein will have not noticeable effect. Other times the change in the protein will result in the protein not being able to function at all. The most drastic effect is when the mutation causes that protein to never be produced at all. 

Keep in mind that not all mutations are devastating. Occasionally mutations can be an advantage. For example, a mutation in the gene that codes for the hemoglobin protein that allows red blood cells to carry oxygen has proven to be an advantage to various people.  Sickle cell anemia is caused by a mutation in the gene that codes for hemoglobin.  A thymine is located where an adenine should be located. This mutation results in the amino acid called Glutamic acid to be placed into the hemoglobin protein in place of the amino acid valine. The change in amino acids results in the formation of crystal-like structures in the red blood cell causing a change in the shape of the red blood cell from circular to a sickle shaped.  The change in shape in the blood cells takes place in the narrow capillaries when oxygen levels are low. The abnormally shaped cell: blocks the capillaries, slowing down blood flow, resulting in tissue damage and pain. Also, sickle cells do not live as long as normal red blood cells.  As a result, the person suffers from anemia. To a person with the trait for sickle cell anemia, the condition is a disadvantage. However, since every trait is coded for by two genes on our DNA, people who have only mutated hemoglobin gene will produce normal hemoglobin have normal red blood cells as well as abnormal hemoglobin that produces sickle shaped red blood cells. In places like Africa where malaria is very common, a person who contains some normal red blood cells and some sickle shaped red blood cells does suffers milder symptoms when they contract malaria. People with all normal red blood cells often die from malaria when it is left untreated. Therefore, in this case, having one mutated hemoglobin gene provides an advantage. 

How do Mutations Occur

Changes in the sequence of nitrogen bases on DNA, or mutations, can occur at various times in the life cycle of a cell. They can occur after cell development due to radiation, steroids, viral infections, or other processes that are able to reach the nucleus and alter the DNA. If these changes occur in cells that are not involved in reproduction of offspring then the mutations will not be passed on to future generations and so are irrelevant to our purpose here.  If the changes do occur in cells involved in reproduction of offspring then it could affect future generations. However, while these types of mutations may be profound, they are not as common as natural changes in the DNA sequences that occur every time an offspring is produced during sexual reproduction.    

As mentioned earlier in relation to Mendel, there are two alleles that carry the code for every trait. This means that there are two genes or segments of DNA that code for the production of every protein made by a cell.  During the production of gametes, sperm and egg cells, the alleles are separated and assorted randomly into separate gamete cells. Because each allele may code differently for a trait this is an obvious source of variation in offspring.  When the gametes are combined during fertilization with that from another organism, there is another obvious source of variation. However, there are even more mechanisms that guarantee variation in offspring.  To understand these variations we must first look at how gametes are produced. 

Cellular Reproduction

All cells reproduce by making copies of their DNA, separating these copies, and dividing their cytoplasm to form new cells. In the case of asexual reproduction, as in the case of prokaryotic bacteria cells, the copied DNA molecule is genetically identically to the original DNA molecule. Therefore, each of the resulting cells is an exact genetic replica of the parent cell.  No genetic variation occurs during this process.  In the case of mitotic cell division that occurs after fertilization, the copied DNA molecule is also genetically identically identical to the original DNA molecule. Each of the resulting daughter

genetically identically identical to the original DNA molecule.  Each of the resulting daughter cells are also genetic replicas of the original cells. It is through mitotic cell division that a zygote grows and becomes an embryo, a fetus, a baby, a toddler, an infant, a teen, and an adult.  Mitotic cell division is also how we repair or replace damaged cells.  Because mitotic cell division involved the creation go genetically identical cells, once an organism's DNA is determined through fertilization, the DNA sequences should be the same in every cell in the organism's body.  The only difference is that in some cells certain genes will be 'turned on' allowing that cell to take on a specific shape and function and other genes will be 'turned off.'

Gametes are produced through a different cellular division process called meiosis.  Meiosis takes place in cells found in the testes and ovaries of animals.  Before meiosis begins, the DNA replicates itself creating an exact copy of its DNA.  The two copies of each DNA strand remain attached at a central location called a centromere.  In the case of humans, there are 46 separate strands of DNA that are wrapped around proteins into structure called chromosomes.  Recall that for every trait there are two alleles or segments of DNA that code for the production of one protein.  Each organism inherited one of the alleles from one parent and the other allele from the other parent.  These alleles are found on what is called homologous chromosomes.  These homologous chromosomes contain the same genes for the same proteins that code for the same traits.  Humans receive one set, 23, homologous chromosomes from their mother and one set, 23, from their father.  After all the chromosomes are replicated in the cell, the homologous chromosomes join together on the nuclear membrane.  An enzyme then cuts a segment of DNA from each of the homologous chromosomes and switches it with the cut segment from the other homologous chromosome. This process is called crossing over and is illustrated in the diagram below. 

Crossing Over

Crossing over provides a major source of genetic variation.  Recall that each of us receive one set of homologous chromosomes from one parent and the other set of homologous chromosomes from the other parent.  Therefore, our mother, lets say, received one set of homologous chromosomes from her mother and one set from her father.  In the formation of the egg that was fertilized and produced us, the crossing over process ensured that we not only received traits from our grandmother but also received traits from our grandfather. 

After crossing over takes place, the cell arranges the chromosomes in the center of the cell in random order.  This random order also provides a source of genetic variation and is the reason we do not look exactly like our brothers or sisters.  After the chromosomes are arranged in a random order they are separated to form two new cells.  In each of these two new cells, the chromosomes are again lined up in the center of the cell and again separated into two new cells.  The end result is four new cells with half the number of chromosomes as the original parent cell.  These cells are called gametes.  When gametes combine during fertilization, the homologous chromosomes are combined creating a cell with 46 chromosomes. 

Recap of Sources of Variation in Cellular Reproduction

The first source of genetic variation during sexual reproduction arises through the crossing over process when DNA segments from each homologous chromosome are switched.  The second source of variation occurs during the random assortment of chromosomes into separate cells during meiosis.  The third source of genetic variation occurs gametes from two genetically different individuals combine their chromosomes to produce a genetically different individual. 

Mutations Resulting During Cellular Reproduction

Mutations can often occur during the crossing over process.  Segments of DNA may be placed on a different chromosome than they should have been.  This would result in chromosomes having deletions of DNA or several genes.  The segments of DNA can also be turned around and joined to the homologous chromosome in a different order than they should have been.  This can result in many genes being altered or just one gene being affected as in the case of sickle cell anemia.  Because there are always two alleles or genes that code for each trait, sometimes the fact that one gene is mutated does not affect the cell because the other allele or gene can still code for the necessary protein.  However, in other cases, the affect may be profound because two many genes are affected. 

Mutations can also occur when the chromosomes are separated during meiosis.  Occasionally, homologous chromosomes fail to separate resulting in gametes with an extra chromosome or gametes missing a chromosome.  Down syndrome is a condition where the gamete contains an extra chromosome resulting in an individual with 47 chromosomes after fertilization.  Turner syndrome is a condition where the gamete is missing a chromosome resulting in an individual with only 45 chromosomes after fertilization. 

Recall that any change in a DNA sequence is referred to as a mutation.  As mentioned above, some mutations result in profound changes in individuals.  Some mutations result in death.  However, some mutations just result in a variation of the expression of a trait.  For example, someone with light skin has genes that code for a low amount of melanin to be produced whereas a person with dark skin has a variation of that gene that codes for a high amount of melanin to be produced.  The variation is not lethal nor a disadvantage.  In fact, a high production of melanin is often an advantage as it helps protect the skin from sunburns.

DNA and Evolution (Part II)




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