Evolution: The Big Picture

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While this post is not going to tell you whether or not to believe evolutionary theory and the ideas and concepts surrounding it, it will hopefully give you a deeper understanding of what evolution is, as well as the evidence and theories that have led to its current understanding. We will discuss how new species come to be as well as how species can adapt over time. We will discuss contributors of evolutionary theory, including some that have been previously mentioned on this blog. Basically, we are going to briefly an thoroughly describe all of the factors that play into evolution. 

As we have already discussed in "Did Darwin Do It All?" there were multiple scholars that contributed to evolutionary theory, many of which also fueled Charles Darwin's research in the Galapagos Islands. These contributors are detailed below with a summary of their most notable work relative to evolutionary theory.

Erasmus Darwin- Proposed that life began from one common ancestor, and that sexual selection led to changes in a species. 

Jean-Baptiste Lamarck- Believed that changes in the environment caused species to adapt so that they could continue to successfully interact with the environment. Adaptions occur in lineage over time as unused anatomical features become "useless".  He also believed that all species that currently exist are adaptions of previous ancestors, and that no species ever goes "extinct."

Thomas Malthus- Believed that competitiveness would eliminate useless features, ultimately leading to natural selection. Competitiveness would be bred through overpopulation. 

Georges Cuvier- Studied fossils to piece together to prove the theory of extinction based on anatomical features. Due to rapid and abrupt changes in the Earth, species would cease to exist as living organisms. 

Charles Darwin- Discovered that shorelines go through many changes due to tectonic shifting, as well as how animals will adapt to their surroundings in order to survive.

Another aspect of evolution is the idea of microevolution, or evolution within a single population. While reading through some of the material I have posted about evolution, you might have wondered about some points that I have only briefly mentioned. To help clear up some confusion, I have highlighted some of the main concepts in microevolution below. For even more information, please visit "Microevolution: Changes In Populations".

Mutation- A gene will randomly change, or mutate, to one that is not present in a set of parents but will appear in their offspring. This rarely happens and will not alter a large percentage of one generation in a population.

Genetic Drift- A seemingly recessive gene will randomly become dominant in the offspring. 

Migration- Organisms from different populations will reproduce, integrating their gene pools.

Natural Selection- Organisms of one type of dominate trait will reproduce with dissimilar organisms more often than with organisms that bear their own traits, and these traits will eventually die out.

It is important to note that while microevolution concentrates on evolution in a specific population, macroevolution focuses on evolution on a much lager scale with multiple populations.

Another interesting measure of comparison in evolution is comparing through homologous structures and analogous structures. Both are detailed below.

Homologous- Similarities in anatomical structure are derived from common ancestors.

Analogous- Similarities in anatomical structure are derived from common function, not ancestry.

Now that we are familiar with some of the terms and history of evolutionary theory, it is time to talk about the evidence that has brought us to our current understanding of evolution.

Biochemistry/DNA- As we learned in "DNA Sequence Comparisons", even species that you would believe vary by extreme amounts have very similar DNA, by more than 50%. This proves that event though species do not seem to be related, there is evidence suggesting that they are at least slightly related. The most compelling case that I have found in which DNA sequence comparison supports evolution is the similarities between humans and chimps. Their genetic code is 99% similar, suggesting that, almost beyond a doubt, humans and chimps have adapted from one common ancestor.

Embryology- As you can probably deduce based on the root of the word, embryology focuses on embryos. Evolutionary embryology shows that embryos follow a common developmental pattern based on their ancestry. Embryos that follow similar patterns share a common ancestor. As the embryos grow, differences that distinguish them as adults become more apparent.

Fossil Record- Fossil records show us what traits many organisms once carried, and how they relate to species present today. As fossils are preserved in the layers of the Earth, we are able to construct a timeline of how species adapted over time to become what we know today. We can see natural selection frozen in time, as certain traits died off.

Comparative Anatomy- Comparative Anatomy evaluates the similarities of physical structure between two ore more species to determine their relativity to one another. The higher percentage of similarities that a set of species have, the higher the possibility that the animals share a common ancestor.

As you can see, evolution is a highly debatable topic, however, there is a large amount of evidence supporting evolutionary theory. It is very difficult for me to take a dedicated stance on the issue, as I see both pros and cons to the topic. I very strongly believe that organisms are constantly adapting and changing, and that the organisms we see today are variations of organisms that have existed in the past. This is clearly shown through DNA comparisons, as many species have extremely similar genetic codes, so much so that it is difficult to reasonably deny the possibility of a common ancestor. There are also reasonable theories that explain patterns that can be seen through fossil records and behavioral patterns alike that would support evolution. However, I do not believe that all species can be traced back to one common ancestor, such as the ever popular "single-celled organism" theory suggests. There is too much variation for this to be correct, in my opinion with the knowledge I currently possess. Regardless of my opinions, this was an extremely intriguing topic to research, and I hope that you enjoyed it as much as I did.
To conclude (and because I couldn't resist):

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Microevolution: Changes in Populations

For this post, we are going to use two different sources to research microevolution, and then answer some questions about the materials explored.

For the first part, we are going to explore Berkeley's information here. According to Berkeley, microevolution is evolution on a small scale, within a single population. They also define a population as a group of organisms that interbreed with each other and share a gene pool. There are four different mechanisms for evolution:

Mutation
Certain genes randomly mutate to another variation of gene, presenting a completely different trait than its predecessor.

Migration
Organisms from different populations will reproduce, integrating their gene pools.

Genetic Drift
When organisms reproduce, recessive genes randomly become dominant in the offspring.

Natural Selection
Organisms of one type of dominate trait will reproduce with dissimilar organisms more often than with organisms that bear their own traits, and these traits eventually die out.

There are many examples of microevolution, however, we are only going to look at three of them. The first example is the size of the house sparrow. Since 1852, the size of the American house sparrow has become longer, most likely as a cause of natural selection as the sparrows have had to adapt to the decreasing temperatures of their environment. Another example is how enterococci bacteria have become resistant to some antibiotics. Many other organisms have also built up a resistance to herbicides and pesticides. For the last example, we are going to look at how organisms have coped with global warming. While many organisms stay dormant during the winter, halting reproduction and growth, longer summers allow them to take advantage of the temperatures and accomplish what cold temperatures don't allow them to. This does, however, require evolutionary change.

For the second part of this post, we are going to use this resource.

After viewing the simulation, there are a couple of questions raised that can be connected to the larger question: Why are some guppies brightly colored, even though it makes them more visible to predators? These questions can reasonably include: Why do some guppies tend to be more colorful or drab? What role does color play in survival? What is the push and pull that the environment has on the correlation of guppies in Endler's pools?

As we can see from the simulation, when a predator is present in the guppies' environment, they blend into their surroundings, similar to how a chameleon will change color or a moth will have certain patterns on their wings. It is a mechanism of survival; if they can't be seen, they won't be hunted and will therefore survive. However, when a predator is not present, bright coloring appears in the guppies. This is because brighter coloring will attract mates, which will lead to a larger population of guppies. The larger the population, the higher probability of species survival. This situation is similar to the bright coloring in male peacocks and ducks.  As you can see, there is a strong push/pull factor when it comes to survival in an environment, and a balance must be reached to obtain a proper morality rate for species survival.

I hope that you now have a better understanding of microevolution and how it plays into the survival of a species; I know I do!

DNA Sequence Comparisons Between Species: Molecular Evolution

Recently, we have been working a lot with genetics and evolution, so for this post, we are going to combine the concepts to observe the similarities in DNA between multiple organisms, particularly through a beta globin gene that all of the organisms produce.  To accomplish this, we used a program, Biology Workbench, to compare the genetic code of humans, chimps, goldfish, chicken, mice, and wallabies. The program highlighted the similarities between the codes in blue, the differences in black. The results are shown below. 

By analyzing the data from the comparison of chimp DNA to human DNA, we see that the chimp has 600 base pairs while humans have 626. Similar nucleotides in both sequences are represented through blue asterisks, and are known as "conserved" nucleotides. By referencing the data from the human/chimp comparison, we see that the sequences have a 99%  similarity. Because the sequences do have such a high similarity, it can be reasonably concluded that they would share a very similar protein structure as well. In contrast, the similarities between humans and chickens are remarkably lower at 57%. From this, we can expect humans to produce beta globin that is more similar to that of the chimp rather than the chicken.  We can also see that the results achieved from this alignment support the results on evolutionary relationships, as anatomical structure and protein structure similarities connect relationships between chimps and humans.

The diagram below examines all of the species' sequences that were compared through the computer program. Because the species that were compared do not share a common ancestry, an unrooted tree diagram was used to compare the species. When viewing the diagram, you should understand that the closer the branches are to each other, the more closely related the species are, and conversely: the farther the distance, the farther the relativity.

As you can see, the two shortest "leaves" on the diagram belong to the human and chimp, and the both extend from the same branch. This means that they are the two most closely related species on the diagram. Conversely, the two species with the least relativity are the chicken and human, as they are the farthest apart on the diagram. Listed below are the other similarity percentages between humans and the other compared species.

Human:Chimp- 99%

Human:Chicken-57%

Human:Mouse- 79%

Human:Wallaby- 75%

Human:Goldfish- 63%

It is very interesting to see that even though there are few species even relatively close to humans, all of them lie above the 50 percentile in comparison of their DNA structure. This also shows that mammals in the rodent family are much closer to primates than other species.

While we have already discussed the unrooted tree diagram, it is also important to mention and demonstrate the use of a rooted tree diagram. While rooted tree diagrams are used to compare species that share a common ancestor, the animals we are comparing today do not, and thus we will leave that section of the diagram unlabeled. The rooted tree diagram does, however, allow us to see more clearly which species have descended through generations.

As you can see from the diagram, the goldfish is most closely related to the chicken while chimps and humans are most closely related to mice.

Homology is defined as a similarity in a feature that exists in two or more species due to descent from a common ancestor of the species. As we can see in this diagram, chimps and humans share the greatest homology with respect to the beta globin gene.

Another aspect of the diagram we should discuss are nodes. Nodes are branching points in the diagram that represent divergence fro a common ancestor. Based on the diagram above, we can conclude that chimps and humans have the most ancestral nodes, as they have diverged three times. This proves that both humans and chimps have adapted from their common ancestors. We can also determine that humans and chimps have diverged most recently, while the wallaby and mouse developed least recently. This can be determined based on the amount of nodes present in the diagram.

Now, let's try to imagine what the order would be if a kangaroo were to be compared to the species already present. It is reasonable to believe that the kangaroo would be in a similar location to the wallaby, as they both carry similar characteristics.

While sequence data can be very helpful in identifying relations between species, there are at least three other methods that can be used to determine evolutionary relationships as well.  These can include environmental interaction, geographic location, and physical features. By evaluating the similarities between how species interact with their environment and the behaviors they exhibit, it can be understood that there is a possibility that the species are related, or have descended from a common ancestor. This possibility can also be explained through physical features, as parallels between a species' traits can explain connections to other species and a common ancestor. Geographic location can determine evolutionary relations, as relative location can express how a species, and others that are similar, interact with their environment and how they relate globally.

It is amazing to see how genetics relate to evolutionary theory, and how similarities in species can be examined.

Did Darwin Do it All? Explanations of Evolution

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As we are already aware, in order to achieve maximum scientific advancement, the contribution of multiple parties is required. This is true in all forms of science, including that of evolutionary theory. Charles Darwin is notoriously known as the creator of evolutionary theory, and while he made extremely large contributions to the research, he is not the sole individual responsible for the creation of evolutionary theory. For this post, we are going to investigate the roots of evolutionary theory to gain a deeper understanding of this topic.

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To begin, we are going to travel back two generations before the birth of Charles Darwin to Erasmus Darwin, Charles' grandfather. Erasmus Darwin was one of the revolutionary leaders of evolutionary theory, and his findings helped fuel Charles Darwin's research. Erasmus was a man of many trades,  acting as a physician, poet, philosopher, botanist, and naturalist.  He was also well versed in knowledge regarding topics such as paleontology, biogeography, systematics, embryology, and comparative anatomy. He began to discuss the possibility of life originating at one ancestor, forming one living filament. He also discussed how changes could occur in species based on competition and sexual selection. Through this, it became clear that the strongest members of a species would reproduce, passing on the strongest traits, and the weaker traits would eventually die out. 

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Another large contributor to the advancement of evolutionary theory was Jean-Baptiste Lamarck. Though he was, and still is, largely discredited for his work, his theories led to what is the current evolutionary theory today. Charles Darwin and other notable scholars held him in high esteem. Darwin even stated that Lamarck was the first man to arouse attention to "the probability of all changes in the organic, as well as in the inorganic world, being the result of law, and not of miraculous interposition." Lamarck was the first person to take an actual stance on the topic, declaring that changes in the environment forced changes in the species surrounding it so that they may survive. Disuse of an anatomical structure caused it to shrink and eventually disappear from the gene pool. This theory differs vastly form Charles Darwin's, however, it leads to the same conclusion that adaptions occur in lineage over a period of time. Lamarck even began to question natural selection, though it was not explored much past the idea of a concept. Lamarck believed that evolution dealt with perfection, and was not driven by chance. He believed that all species that currently exist merely evolved from previous species, and that there was no such thing as extinction. Though his ideas vary from Charles Darwin's, Darwin researched his work thoroughly and elaborated on his concepts. 

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The next notable contributor to evolutionary theory that we are going to discuss is Thomas Malthus. Malthus presented even another perspective of evolution. He proposed the idea that overpopulation would lead to famine and poverty, which would eventually consume the human race. This perspective eventually led to Darwin's theory of Natural Selection. Darwin, along with Wallace, determined that overproduction would create a competitive environment, and that variation within a species would produce individuals that faced a higher chance of survival. The perspective offered by Malthus is very similar to what can be seen in Modern China, as overpopulation has led to famine and poverty, and the Chinese government has made an attempt to control birthrates and overpopulation. 

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Georges Cuvier, another contributor to the advancement of evolutionary theory, believed that organisms worked as integrated wholes, and that no part of the organism could change without impairing function. Through the study of many fossils, particularly those of elephants, he developed the basic idea of species extinction. He determined that Earth had gone through abrupt changes that could have wiped out a number of species. Due to Cuvier's work, extinction became a fact that all future scientific theories of life had to explain, including evolution. 

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All of the aforementioned scholars led Charles Darwin to the research that he himself conducted.  This includes his time spent at the Galapagos islands and the information he was able to gather there. What a lot of people don't realize is that Darwin didn't focus sole on the evolution of animal species, in fact, one of his first discoveries was that raised beaches are caused by earthquakes. He realized this with the discovery of rocks that had recently been underwater, but had been moved up-shore after an earthquake. This was evidence of geological change. He also realized that animals would have to adapt accordingly to this change in environment. Another interesting discovery that Darwin realized when he returned to England from the Galapagos was that a finch's beak will adapt to its diet and environment. If one of these factors changed, so would the finch's beak, accordingly. There are, however, no records of where each observed finch originated. One other notable observation that occurred during Darwin's time at the Galapagos islands was the distribution pattern of mockingbirds in the Galapagos islands. Darwin noticed four different mockingbird variations, with one distinct variation located on each of the three islands, and one variation that was found on all three. Darwin became curious as to why there would be separated species on each island, if each island was similar to the ones surrounding. 

Isn't it amazing how your ideas can inspire others? 

Bacterial Transformation Lab

As we learn more about DNA, there are any different concepts we can question and explore. One such concept is genetic transformation, which we explored as a class. This was done through a lab experiment in which we introduced plasmid into an E. coli bacteria colony in an attempt to alter the DNA. To gain comparable data, the following conditions were tested in separate agar plates:

1. +pGLO (plasmid), LB (nutrient), and Ampicillin (antibiotic)

2. +pGLO, LB, Ampicillin, and Arabinose (sugar)

3. -pGLO (no plasmid), LB, Ampicillin

4. -pGLO, LB

To begin the lab, we used a sterile pipette to transfer 250 ul of transformation solution into separate tubes containing +pGLO and -pGLO. These were then put on ice. Using a sterile loop, a colony of bacteria was added to each tube while they sat on the ice. Plasmid was then added to +pGLO only, not -pGLO. Both tubes were then incubated on the ice for 10 minutes. After this time, the tubes were transferred  to a heated water bath for 50 seconds, then immediately placed back on the ice for 2 minutes. 250 LB nutrient broth was added to each tube, then incubated for another 10 minutes at room temperature. 100 ul of the transformation and control suspensions were added onto the appropriate plates. The suspensions were spread evenly around each plate, and then incubated, upside down, at 37* C, for 24 hours. 

After placing the plates in the incubator, but before data was collected and analyzed we were asked to answer the following questions:

1) On which plates would you expect to find bacteria most like the original non-transformed E. coli colonies originally observed?

I would expect to find bacteria growth most similar to the original colonies in the plate "-pGLO, LB". I predict this because it has the bacterial cultures, but doesn't need to fight the ampicillin in order to grow.

2) If there are any genetically transformed bacterial cells, on which plate(s) would they most likely be located?

I predict that any genetically transformed cells would exist on the plate "+pGLO, LB, Amp, and Ara". This is because the bacteria has to fight the ampicillin while still being able to survive, which would only be possible if the bacteria had transformed.

3) Which plates should be compared to determine if any genetic transformation has occurred?

All of the plates should be compared to plate "-pGLO, LB" to determine transformation, as "-pGLO, LB" most closely resembles the original colonies. 

4) What is meant by "control plate"? What purpose does it serve?

A control plate is a plate that is not affected by any variables; it's results can be relied on to compare transformation data. 

The results from the experiment are displayed below.

The chart above details which dishes had cellular growth as well as which had the ability to glow. As you can see, the data aligned with the original hypothesis. 

Another hypothesis proven correct was that the +pGLO, LB,Amp, and Ara plate would contain the transformed bacteria. The reasoning behind the hypothesis is the same reason as to why it was proven correct.

It is very difficult to see in this picture, due to the lighting, however, this plate shows significant bacterial growth; nearly the entire plate is covered. 

It is amazing to see how genetic transformation occurs, and what factors determine the traits of bacteria cultures. This was a very interesting process that was incredible to witness first-hand. It has allowed me to understand genetics with a different perspective than I had had before. 

Personalized Genomics: Do You Want To Know?

As technology and knowledge of DNA is advancing, the possibility of personalized medicine is becoming more and more realistic. We are growing closer to the day and age where we will be able to send DNA samples to companies where our genomes will be analyzed to predict any diseases and health issues that we may come across in our lifetime. The big question surrounding this topic is, "Would you want to know?" Would you want to know your chances of getting cancer or Huntington's Disease? Would this help you seek prevention and make you become aware of your health, or would knowing this information cause your life to be controlled by dread? How would your family members and close friends react to this information? These are all really important questions to ask when trying to envision this topic.

This topic makes me reflect to GATTACA, and how when Vincent was born, the statistics of his life were presented on the screen. He had a 99% probability of heart dysfunction, and was told that he would die in his 30's. Personally, I do not believe I would like to know this information. I find comfort in fate, and believe that knowing this information would cause me to fear life itself, constantly worrying if my actions could cause me to die at an early age. It is very important to be healthy and take care of yourself, but like all things, this can be taken to the dangerous extreme.

In an article from USA Today, Kristin Power's decision to test for Huntington's Disease is described in detail, covering all aspects from emotional to scientific. She explains how making this decision was difficult, but it was something that she felt she had to do. Her brother is less willing to be tested, however, he is still considering it. Kristin has enrolled in counselling to cope with the stress, even before she has been tested. There is no way to measure how much emotional strain will come from this test, and if Kristen tests positive for the gene carrying the disorder, she will have to work to make this a part of her life. She has already considered this, stating that since Huntington's is hereditary, she will not have children if she tests positive. In addition, even if Kristin tests positive, there is the possibility that the test was inaccurate. In similar cases, people can forget that genetics are only one component to health; your actions can still impact your medical future. For example, if you test negative for skin cancer, you can still be diagnosed with it if you expose yourself to strong radiation.

This is a very interesting topic that definitely requires some thought; would you want to know your medical future? To view the article about Kristin Powers, please click here.

DNA Fingerprinting: Using DNA for Identification

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As we learn more about DNA, we should apply these concepts to practices used in current sciences. One field that works with DNA on a daily basis is forensic science. Even though 99% of human DNA is the same, the 1% difference causes each person's DNA to be unique, except for that of unusual births, such as twins. By testing tissue samples with gel electrophoresis, a person's DNA code could be discovered, and if the results matched to another set of DNA, then the specific person could be identified. This is applies to forensic investigations in that if DNA is found at a crime scene, it can be matched to a suspect. Since the discovery of DNA technology, multiple people convicted of crime have been exonerated based on DNA evidence. Since this is such an interesting application of science, we are going to explore this topic more through an activity using this source.

To begin with, we are going to read about and analyze the events surrounding the murder trail of Dr. Sam Sheppard.

1. In your opinion, what role (if any) did newspaper stories and editorials have in the outcome of the original trial of Dr. Sam Sheppard?
As I read through the chronicle of events, it became clear to e that media and press coverage played a significant role in this case. A majority of the headlines presented a very biased stance on the trial, pressuring officials to take action. It is usual for this to occur in a murder investigation, but not to this extent. This coverage also caused the jury to have a bias toward the case; there were multiple occasions in which a juror questioned the judge on a topic that had only been discussed in the media, which proved to be false.

2. What is the function of the restriction enzymes in DNA fingerprinting?
Restrictive enzymes, when mixed with DNA, cut molecules at different lengths based on their genetic code. For example, one specific enzyme will cut the DNA when the code "GAATTC" is read. Since everyone's DNA is different, the lengths of these cut sections will differ as well.

3. What is the function of  the agarose gel electrophoresis step?Agarose gel electrophoresis acts as a "molecular strainer", sorting the longer strands of DNA from the shorter strands by the use of positive and negative charges. The shorter strands of DNA will move through the gel much more quickly than the longer strands.

4. Why is a nylon membrane used to blot the DNA?
The nylon membrane is much easier to handle and work with than the agarose gel, and makes viewing the DNA more manageable.

5. What does a dark spot on the X-ray film indicate?
The dark spots on the film represent where the probes sat, attached to the DNA. Together, the spots form the DNA fingerprint.


For the second part of this activity, we are going to use this source. We are going to analyze the case of Ronald Cotton's wrongful conviction, as well as the case of O.J. Simpson.

6. What evidence was initially used to convict Cotton?
Originally, an eyewitness account was used to convict Cotton. When the victim had to identify her attacker, he was not in the line up of suspects, so she selected the person who bared the closest resemblance, which was Ronald Cotton.

7. What did the DNA evidence show?
By using DNA evidence, it became clear that Cotton was innocent, as well as the fact that often times, witnesses are unreliable. This has led to prevention of wrongfully convicting the innocent in the present.


8. How could DNA fingerprinting be used to prevent a false conviction if a case like this was being tried today?
DNA fingerprinting eliminates the chances of convicting the wrong person by ensuring correct identification. It ties a specific person to the scene of a crime without a doubt.

9. What percentage of convicts are unjustly convicted of sexual assault cases, according to Neufeld and Scheck?
According to Peter Neufeld and Barry Scheck, approximately 25% of convicts are unjustly convicted of sexual assault.

10. The O.J. Simpson trial was one of the most visible trials that attempted to use DNA evidence.  In the end, the DNA evidence was not satisfying to the jury, who acquitted Simpson.  What do Neufeld and Scheck believe about the impact of the O.J. Simpson trial on the use of DNA evidence?
Both Neufeld and Scheck believed that O.J Simpson's case showed potential for DNA evidence in forensic cases, however, when the technology is mishandled, it is not useful in the case. When presenting DNA evidence, there can be no room for error.


Overall, DNA evidence has proven very useful in multiple cases, both cold and current. It is amazing to see how science can be applied in different fields, as well as how far technology has advanced.