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.

New School DNA Sequencing: Bacterial ID Lab

Using the "Old-School" Sanger method has been very useful, however, there is another, more recently developed method that has proven far more efficient. This new method is used in modern molecular biology labs as well as forensic investigations. To completely explore this method, you can use the online virtual lab here.

As I worked through the lab, I answered the following questions so that I could gain a deeper understanding of the activity.


1. As the medical technician in charge of this investigation, what are you trying to determine about the tissue sample provided to you?
As a lab technician, I am trying to determine what bacteria is contained in the tissue sample.

2. How did you prepare the DNA to be used in this investigation?
During the investigation, the DNA was prepared by adding digestive enzymes and buffers to a bacterial sample. The microcentrifuge tube containing the sample sat for several hours, and was then heated in order to activate the digestive enzymes. Once the sample was denatured, the sample was placed in a centrifuge to remove cellular debris from the sample.

3. Describe how PCR is used to make copies of DNA sequences.
PCR causes a reaction that can be tested by comparing positive reactions to negative reactions. By running the sample through various temperatures, the double helix structure of the DNA was unwound and separated into single strands, where it was then copied by the DNA polymerase.

4. Summarize the technique used to purify the PCR product.
To purify the PCR product, more buffer is added to the sample.The remaining PCR product is placed into a column and then into a centrifuge, so that only the long lengths of PCR remain with the sample of DNA. While in the column, the product is separated from the non-useful components, and then again when the DNA is separated from the rest of the product. 

5. What is produced during the sequencing prep PCR run?

During the sequencing prep PCR run, the DNA was prepared in 12 sequencing brews that contained primers, buffers, polymerase, nucleotides, and florescent-tagged terminators. This produced multiple DNA strands that varied in length.

6. Describe how the automatic sequencer determines the sequences of the PCR products.
The automatic sequencer determines the sequences of the PCR products through Gel Electrophoresis, where the samples are exposed to positive and negative electric charges. Since DNA contains a negative charge, it is carried to the positively charged area, expressing the notion that "opposites attract". The molecules are separated based on their size. Where they cease movement in the gel, scientists are able to read these bands as the basic genetic code: G,C, A, or T.

7. What does BLAST stand for?
BLAST is an acronym for "Basic Local Alignment Search Tool".

8. What conclusions did you make using the results of the BLAST search?  Did these conclusions support a clinical diagnosis for the patient (what disease did they have)?
After analyzing the results from the BLAST search, it can be concluded that the patient had Bartonella henselae.

I hope you enjoyed this lab as much as I did, while gaining insightful information about DNA sequencing.

GATTACA Reflection

"There is no gene for the human spirit."

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In class, we recently watched the movie GATTACA to evaluate the effects of science and technology upon society. The movie expressed a very intriguing plot in "the not-so-distant future" where the "best" genes can be selected to produce exceptional offspring. Everything can be determined from eye color to the probability of alcoholism. It is still possible to produce children without the use of selective genetics, but the results are considered impure. How does this fictional world compare to the one we are advancing towards? To reflect on the teachings of GATTACA, there are a few questions that we can analyze.

1. The following terms (de-gene-erate, In-valid) were used in the movie. How do they relate to the words we use: degenerate and invalid?

      The words are very similar, but relate more closely to genetics. They take terms tat are used commonly today and applied them to a negative tone to describe human beings that carried less desirable traits.

2. Why do you think Vincent left his family, tearing his picture out of the family photo, after winning the swimming race against his brother?

When Vincent overcame his brother physically, he became re-born in the sense that he realized his potential. All his life, leading up to this point, he lived in the shadow of his brother, and when he realized he didn't have to, he felt he had to cut all ties to the life where he lived in restraint. He had to pursue a future where he could live as he wanted.

3. Describe the relationship between Vincent and Anton.

Vincent and Anton have a very interesting relationship that deals with the conflict of average sibling rivalry in addition to the competition for affection based on the imbalance of their genetic situation. (Vincent was conceived naturally while Anton was conceived through selective genetics.) In the present, they also must understand life from the other's perspective, Vincent coping with having nothing expected of him and Anton having everything expected of him.

4. When Jerome Morrow said to Vincent/Jerome, “They’re not looking for you. When they look at you, they only see me,” what did he mean? Can you find any parallels to this type of situation in real life?

Jerome meant that his name had become an idea, not a specific person. By losing his ability to lose his legs, he lost his identity. When Vincent gained Jerome's name, he acquired a world of possibility. Jerome's name had become nothing but a label for a perfect genetic code. This is very similar to things we see in reality, most often in celebrities. When people talk about celebrities, they almost always seem to forget that there is a real human with real emotions attached to the name.

5. Choose your favorite character from the film. Explain why you choose that person. Would you want to be that person? Why? Why not?

My favorite character from the film was Jerome Morrow. He added a sense of humility to the film, showing that there is a part of life that genetics cannot change or predict. He showed that being perfect is not possible. Personally, I would not like to be Jerome, but I am humbled by his story.

6. At the end of the film, you are told that the Doctor knew about Vincent all along. Why did the Doctor go along with the fraud? What would you have done if you were the Doctor?

The doctor went along with the fraud because he understood the importance of being human. He empathized with the trails of living with imperfect genetics, and decided hat Vincent deserved a chance to pursue his aspirations. If I were in the same position the  doctor was in, I would have acted in the same fashion.

7. The technology to do what was done in the movie is definitely possible within the next ten years. Do you think that Vincent’s world could eventually happen in America? Why?

I believe that unless America begins to realize that human life revolves around more than genetics and a spark of electricity, and that life is not an experiment,  the world of GATTACA will easily become a part of society.

8. What do you think is wrong with the society portrayed in "GATTACA"? What is right?

The society of GATTACA is beneficial in the sense that human life will be lengthened and that hereditary diseases will be eliminated. The issues of this society lie in desensitization and the belief that all life can be controlled.

9. What were the screenwriters trying to tell us through the episode of the 12-fingered pianist? Is anything wrong with engineering children to have 12 fingers if, as a result, they will be able to make extraordinarily beautiful music?

The screenwriters were trying to portray how even perfection has flaws. Engineering children to have traits specific to a profession is wrong because it is trying to decide your child's fate for them. This cannot be justified by the outcome.

10. How does the society portrayed in GATTACA resemble the type of society that some Americans were hoping for during the height of the Eugenics movement?

The Eugenics movement was very similar to GATTACA in that the ambition was to select only the "best" genes, eliminating the imperfect ones. Every person would be a "model citizen".

Old School DNA Sequencing: Sanger Method

Before modern technology was available, DNA sequencing was much more tedious and difficult. In the 1950's Dr. Frederick Sanger determined the sequence of amino acids in protein.  This led to the understanding that DNA sequencing was collinear to the sequencing of amino acids. In the 1970's, Dr. Sanger developed a method to determine the exact sequence of nucleotides in a given gene. This method involved placing the DNA sample in  gel that was charred both negatively and positively. The longer strands of DNA would be pulled through the gel slower than the shorter strands, and the DNA separated into bands. The band positions were then "read" in order to determine DNA sequence. To stimulate this, we were given a lab packet in which DNA from four different subjects were tested. We were asked to read each sequence, compare them, and finally determine which subjects carried a disease. Pictures from the lab are posted below. 

In the step above, we determined the sequencing of each subject's DNA by evaluating the bands. This data was then placed in the chart pictured in the last image. 

After comparing the data, it became clear that "Norm" was the only healthy patient. All other subjects showed some disturbance in their DNA that caused them to be effected by the disease. Carol experienced a front shift mutation, Bob experienced a truncation mutation shift, and Abby experienced point mutation. This disease would be unrecognizable were it not for the Sanger Method.

DNA Extraction Lab

As we learn more about DNA, it is great to apply the concepts we learn so that we can gain an even deeper understanding. In this post, I am going to describe a lab we did in class in which we extracted DNA from wheat germ. In order to do this, our instructor had us work in groups so that we could collaborate our knowledge.

To begin the lab, we measured out 1 gram of raw wheat germ. This germ was then placed in a 50 ml test tube where it was mixed with 20 ml of hot tap water for 3 minutes. After being stirred, 1/4 teaspoon of detergent was added to the mixture. This was again stirred. 5 minutes after adding the detergent, we added 14 ml of alcohol. This was done very carefully so that the alcohol would not mix with the germ mixture. This was necessary in the extraction process, as DNA precipitates at the water-alcohol interface. The image below shows this step being done.

After doing this, the test tube had to sit for a few minutes so that the DNA could precipitate. After a short wait, we collected the DNA by using a wooden stick.

Overall, this was a really fun lab that expanded my knowledge of DNA.

From DNA to Protein: The Central Dogma

As we are aware, DNA is found in protein, but how does it get there? After all, DNA is located in the nucleus of all cells, and ribosome build protein. In order to cross the nucleus membrane in order for protein to be made, there has to be a step in-between that will transfer the DNA code to the ribosome, but what is that step? The answer lies in the process of the central dogma, and the material RNA. RNA, as you can predict, is very similar to DNA. Instead of having dioxyribose material, like in DNA, RNA contains ribose. As we will learn, RNA will be the key component to the central dogma, allowing protein to be successfully made. For now, we are going to define a few terms related to this process. To view the vocabulary, please click here.

DNAi Timeline

Like most things, DNA would not be as well understood as it is today without the contributions from multiple researchers. This post is going to detail the work from some of these contributing scientists that helped develop the current understanding of DNA. A great resource for information on other scientists that contributed work to the evolution of the idea of DNA can be found at this address. This is also the resource that was used for this post.

Martha Chase, Alfred Hershey, and the "Blender Experiment"
In the early 50's, a group of researchers at the Cold Spring Harbor Laboratory were researching bacteriophage genetics (also referred to as phage genetics). Phage are viruses that target, attack, and infect bacteria. At this time, it was already known that phage was constructed with an outer casing of protein that surrounded in inner core of DNA. It was also known that phage relied on bacteria to reproduce, and that phage attached themselves to bacteria by their tails. It was hypothesized that after attaching, the phage pumped genetic material into the bacterial host, causing the bacterial enzymes to be replaced by new phage particles. In 1952, Martha Chase and Alfred Hershey dedicated their work to discovering why the bacteria transformed into a phage producing organism, proving whether or not DNA was a transforming principle. Through chemical analysis, it was discovered that DNA contained high amounts of phosphorus and zero amounts of sulfur. This information was in contrast to the known information about protein, which contains sulfur but no phosphorus. This information was used in an experiment to test which component entered the bacteria for infection. This was designed in a way that radioactive phosphorus (32P) and radioactive sulfur (35P) to selectively label the phage DNA and protein. The radio labeled phage was then combined with unlabeled bacteria so that the phage could attach. The attachment was then disrupted as the culture was mixed in a Waring blender. The samples were then spun in a centrifuge in an attempt to separate the phage from the bacteria. This attempt was successful, and due to the fact that the phage is lighter than the bacteria, it remained suspended in the test tube while the bacteria collected at the bottom in the form of a pellet. After evaluating the sample 35P, it was discovered that the newly produced phage from the bacteria did not contain any radioactive sulfur, unlike the protein coat of the parent phage.  In contrast, the sample 32P contained newly produced phage from the bacteria that was contaminated with radioactive 32P. From this, it was determined that phage DNA was used inside the bacteria to produce new phage, confirming that DNA is the genetic material.

http://upload.wikimedia.org/wikipedia/commons/thumb/3/32/Hershey_Chase_experiment.png/357px-Hershey_Chase_experiment.png

DNA Sketch Model

As we work further into the human body and system, we must work to understand one of the most key components to human function: DNA structure and function. To do this, we were given instruction about the basic components to DNA and asked to fit them together in a sketch that would demonstrate how it fit together to form a strand of DNA. The pictures included below are the "finished product" of this activity.

As you can see in the last picture, a nucleotide is shown. A nucleotide is the basic component of DNA, composed of dioxyribose, phosphate, and one Guanine, Cytosine, Adenine, or Thymine. Notice the "or" in that list. A nucleotide only contains one of the four listed, and can be found int the acronym GCAT. These then form a hydrogen bond with the opposite strand; the only possible combinations of pairings are Guanine with Cytosine, and Adenine with Thymine. Once the strands are bonded, they align themselves in a double helix shape, forming the common DNA perception. There you have it: the basics of DNA!