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Molecular Clocking Paper

Submitted by jhussaini on Wed, 02/20/2019 - 23:12

The paper investigates the divergence of cephalopods. The limited fossil record makes it difficult to find divergence times and patterns. The researchers used molecular clocking, a technique to track the timing of when groups in the cephalopod phylogeny split off from one another. Molecular clocking measures genetic mutations over time in different groups to show measure how they evolve differently, and this data is subsequently compared to their fossil records. The paper showed that cephalopods diverged during the Mesozoic Revolution, 160-100 millions of years ago. During this time there were not only dinosaurs above land, but there were also dramatic changes below the sea caused by competition. Many adaptations arose around this time in response to the competition. For example, cephalopods lost their shells, which made them more lightweight and improved their agility. Predator-prey arms races influenced many of the adaptations that arose among cephalopods. The researchers tracked when these adaptations came into existence in different groups in addition to the rate of diversification.   

Molecular Clocking Paper

Submitted by jhussaini on Wed, 02/20/2019 - 23:12

The paper talks about the divergence of cephalopods. The limited fossil record makes it difficult to find divergence times and patterns. The researchers used molecular clocking to figure out where groups split off from one another. Molecular clocking measures genetic mutations over time in different groups to show measure how they evolve differently, and this data is subsequently compared to their fossil records. Cephalopods diverged during the Mesozoic Revolution, 160-100 millions of years ago. During this time there were not only dinosaurs above land, but there were also dramatic changes below the sea caused by competition. Many adaptations arose around this time in response to the competition. For example, cephalopods lost their shells. The researchers tracked when these adaptations came into existence in in addition to the rate of diversification.   

cdc20 and Naegleria

Submitted by jhussaini on Wed, 02/20/2019 - 23:07

You could use antibodies specific to cdc20 protein to see if it is expressed in the Naegleria. The primary antibodies would bind to cdc20 (if it is present) and the secondary antibodies would bind to the constant region of the primary antibodies. Using polyclonal antibodies as the primary antibody would be a good idea because they can detect low expressing proteins. If we detect cdc20 protein in our experimental group, then the gene silencing and RNAi didn't work. If we do not detect cdc20, then it was silenced, which is what we expect. In our negative control, since cdc20 is not silenced, we expect detection of it. Antibodies can therefore help us make sure that any changes in phenotype between the negative control and the experimental group are because we silenced cdc20.

Methods

Submitted by jhussaini on Sat, 02/16/2019 - 14:34

Summary of Capturing the Tree and Moss

I took a picture of a tree named “Honey Locust” located to the side of the parking lot next to the Life Sciences Building. I took a few steps away from the tree and captured a wide shot at eye level. The camera was in portrait mode showing the tree in the middle of the frame. The picture was from the ground to the top of the tree before branches extended from the tree. Behind the tree was a gray fence and the Life Sciences Building. The Life Sciences Building stood to the right of the the Honey Locust tree and there was another tree to the right captured in the shot. For the second picture, I stepped closer to the tree just until the words “Honey Locust” came into focus. The Life Science Building was also in the background of this image and the tree to the right of Honey Locust was also present. The lowest two branches extending from the tree were more visible than in the previous picture. Finally, I took a close up image of the tree showing the moss and the bark just below the sign. The tree occupied most of the frame but not all of it. The moss was the focal point of the image. 

Summary of Making the Figure

First, I imported the 3 pictures into Inkscape. Then I set the width of each picture to 500 mm. I aligned the pictures from corner to corner. Then I made a text box of width 40 mm and typed in the letter “a.” Then I made a white rectangle of width 80 and layered it under the letter. I then centered the letter “a” in in the rectangle. I dragged the rectangle with the centered letter to the top left corner of the figure. I repeated this process with letters “b” and “c” for the next two figures. Then I made two freehand lines of width 6. I put a marker on both of them to make them arrows. I put a white filling on the markers. I positioned the first arrow to point to the moss and the second arrow to point to the bark on the tree. Then I exported the file to create a PNG image. I saved this image onto my computer. 

methods draft

Submitted by jhussaini on Fri, 02/15/2019 - 17:02

I took a picture of a tree named “Honey Locust” near the parking lot next to the Life Science Building. First I took a wide shot of the tree from the ground to the top of the tree before the branches extend from it. The tree was in front of a gray fence with the Life Science Building in the background. Then I took a picture of the tree with the camera focused on the words “Honey Locust. ” There is the Life Science Building and a tree on the right that is visible in the background. Next, I took a picture of the tree very close up showing the moss and the bark. This picture did not include the sign on it and the fence is only barely visible to the left of the tree. ​

First, I imported the 3 pictures into Inkscape. Then I set the width of each picture to 500 mm. I aligned the pictures from corner to corner. Then I made a text box of width 40 mm and typed in the letter “a.” Then I made a white rectangle of width 80 and layered it under the letter. I then centered the letter “a” in in the rectangle. I dragged the rectangle with the centered letter to the top left corner of the figure. I repeated this process with letters “b” and “c” for the next two figures. Then I made two freehand lines of width 6. I put a marker on both of them to make them arrows. I put a white filling on the markers. I positioned the first arrow to point to the moss and the second arrow to point to the bark on the tree. Then I exported the file to create a PNG image. I saved this image onto my computer. 

gene-editing debate

Submitted by jhussaini on Fri, 02/15/2019 - 15:56

Indeed, gene-editing when done to an extreme could potentially create barriers between people. When people think about what traits they want their children to have, they make an internal list of genes that are "good" and a separate list for genes that are "bad." Gene-editing might cause people to categorize and rank traits, which would lead to more discrimination. Instead of celebrating our differences, we would be drawn apart by them. I can imagine another eugenic movement arising as a result. 

 
 

artificial selection

Submitted by jhussaini on Fri, 02/15/2019 - 15:55

I agree that artificial selection should be used as a tool in medicine. No one deserves to be born with a life-threatening disease. If we have the capability to prevent that, then we should. But there is a difference between selecting traits to save someone's life and selecting traits based on personal whim. The latter is changing fundamental parts of someone's core identity without their permission. What if a parent designed their kid to have amazing hearing but it backfires by causing anxiety due to noise sensitivity? Or what if a parent chooses for their child to have a beautiful eye color, but it somehow limits the child's visuo-spatial skills? Because many genes control more than one factor I agree that we need more research to be done.

Gene-editing

Submitted by jhussaini on Wed, 02/13/2019 - 17:11

I would advocate for genetic modifications to prevent disease. Some people might argue that gene-editing technology is unnatural and interferes with natural evolution. To this I would argue that humans have already altered their own evolution in significant ways. For example, antibiotics have saved people throughout history from dying of infections, and yet they are also unnatural according to the article ““Pro and Con: Should Gene Editing Be Performed on Human Embryos.” Like antibiotics, gene-editing is also unnatural, but unnatural can be a good thing if it prevents disease and increases human survival. According to the NYT article “These Patients Had Sickle-Cell Disease. Experimental Therapies Might Have Cured Them” clinical trials for sickle cell anemia are already underway and have shown initial success in a few patients. I think there should be more research in gene therapy for single gene disorders such as Sickle Cell Anemia and Cystic Fibrosis than for diseases that are polygenic or have a strong environmental component. The causes of the latter are more complex and might require more than gene modifications to be cured. 

I don’t think we should genetically modify humans for purposes beyond disease prevention. Using gene-editing to select for traits related to appearance and personality to make the perfect human being can come with dire consequences. For one thing, classifying genes as “good” or “bad” is arbitrary. Genes that control psychoticism for example can confer advantages such as creativity or open mindedness (according to the article “How Gene Editing Could Ruin Human Evolution”). The article also mentions that influential people such as Carrie Fisher, David Foster Wallace and Kurt Cobain can benefit society despite them all having psychiatric risks. On a more personal note, artificially selecting genes to make a designer baby would detract from a person’s individuality. According to the Wired article “You’re only human but Your Kids Could be So Much More”, having a baby would turn into a “model building exercise” or a “project.” People would wonder if their successes are because of their own hard work or because they were genetically programmed to succeed. Everyone would choose the same traits that are considered to be the best, and we would no longer be diverse or unique. 

How far should gene-editing go?

Submitted by jhussaini on Wed, 02/13/2019 - 13:45

If it were up to me, I would allow genetic modifications only for disease prevention but I wouldn’t go a step further. To those who consider that unnatural, I would argue that humans have already defied natural evolution in many ways. According to the article “Pro and Con: Should Gene Editing Be Performed on Human Embryos?” we have prevented so many people from naturally falling sick and dying through advances in medicine such as antibiotics. Technology such as Crispr-Cas9 offers a more advanced way to prevent diseases, by editing DNA itself. In my opinion, gene-editing should be the go-to treatment for single gene disorders because it is tackling the issue straight from the source. Clinical trials for sickle cell anemia for example are already underway and have resulted in success with patients reported to show no more signs of the disease (according to the NYT article on sickle cell anemia).

However, I think there should be a limit to genetically modifying humans. Using gene-editing to select for desirable traits to increase reproductive fitness or make life easier for us in general can come with dire consequences. For one thing, genes are not always good or bad, but rather they can be a mix. Genes that cause people to be schizotypal or psychotic may confer advantages such as creativity and open-mindedness, according to the Time article “How Gene Editing Could Ruin Human Evolution.” The article also points out that influential people such as Carrie Fisher, David Foster Wallace and Kurt Cobain have made a positive impact on the world despite them all having psychiatric risks. Selecting for favorable traits is a complex process because it comes at the cost of another trait that could be beneficial. On a more personal note, artificially choosing genes to make a designer baby would take away from a person’s individuality. According to the wired article, “becoming a parent would turn into almost an intellectual exercise” or “project” that would focus on designing a baby rather than naturally giving birth to one. I think it’s important to appreciate our differences and flaws rather than trying to change them.

Complexity of Sponges and Ctenophores

Submitted by jhussaini on Sun, 02/10/2019 - 15:17

The aim of the paper is to investigate the characteristics of Porifera and Ctenophores in order to determine their phylogeny. Characteristics such as physiology, morphology and molecular genetics of these organisms is analyzed to map evolutionary relationships. Because these groups have not been studied extensively, making these relationships presents some difficulty. Studying them from the fossil record is a challenge because they are poorly preserved. Ctenophores are gelatinous and fragile, which makes them harder to collect. The wide diversity of porifera and ctenophores also makes them difficult to characterize. For example, ctenophores are found throughout the ocean from pole to pole. Though even with more information collected on the two species, they are often interpreted in the context of bilateria, which leads them to be labeled as less complex than they actually are. Despite the seemingly simple morphology of sponges, they have a similar genetic inventory to more complex animals. Even though the physiology of sponges is different, it carries out the same tasks and is just as complex. 

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