Fire Corals

After looking at the different phylum from the Invertebrates Part 1 Vodcast, I was drawn to the phylum Cnidaria. One organism I found interesting was fire corals. Fire Corals are classified as Hydrozoa in the Cnidarian phylum. They use their long hairs that protrude from their skeleton to trap their prey and get their food from a symbiotic relationship with microscopic red algae called Zooxanthealle. Then they produce clusters of stinging cells that inflict the stings on human skin. I now know why when people go snorkeling and hit a coral reef, they get long lasting scars. Their polyps reproduce asexually, and are near microscopic size and mostly are embedded in the skeleton and are connected by minute canals.  These corals contain gastropores and dactylopores, that are visible on their smooth surface. Fire corals can reproduce asexually through fragmentation. However their brittle skins are easily to be broken during storms or by divers. This relates to learning about the phylum Cnidaria in the Invertebrates Vodcast, where we learned that Cnidria is classified by having specialized tissues. 

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Unit 8 Reflection

Unit 8 was all about evolution, how all the species, and the earth itself, have changed over time. We learned about what exactly was the definition of evolution and how it was measured. All the alleles that make up genes in population are called the gene pool. The frequency of an allele in the population is called allele frequency. Evolution is measured as a change in allele frequency in the gene pool, so all species are constantly evolving. One allele becomes more or less frequent due to natural selection. Natural selection ultimately ends up choosing the genes in individuals that are more likely to survive and reproduce, therefore, making the population look like the "winners". In the Hunger Games Lab, which was the main lab this unit, we saw the disappearance of stumpys over time. They had undesirable characteristics, and therefore did not get a chance to survive and reproduce. The pinchers, on the other hand, grew more in the population because they had the most desirable characteristic to pick up food (using their thumb and index finger).
Natural selection also works in different ways. Directional selection is when one extreme phenotype is favored.  As we saw in the bird beak lab, the tweezer beaks were favored since they were the most helpful in picking up food and soon the amount of offspring were mostly tweezer beaks. Stabilizing selection is when intermediate phenotypes are favored. Disruptive selection is when two extreme phenotypes are favored. Natural is not the only thing that causes species to evolve. Genetic drifts are random events that suddenly changes the allele frequency. This change may be either good or bad. Gene flow is the movement of alleles from one population to another. Mutations can cause a change in DNA, and if desirable, will become frequent in the population. Sexual selections that improve mating success but not help the organisms survive better.
Speciation is the creation of new species. Species separate when they are reproductively isolated. This means that the two species cannot reproduce and have fertile offspring. Temporal isolation is when they reproduce at different times. Geographic isolation is when they are physically separated. This is a technique often used with dog breeders. Behavioral isolation is when they have different techniques to attract mates.
The theory of evolution is opposed, but there is evidence to support it. When all organisms are an embryo, they all look very similar. This suggests that we all share a common ancestor. We also have features that helped our ancestors or that they had, such as our tailbone which shows that we used to have tails. Some organisms have same structures with different functions (homologous). Others have different structures with the same function.
 To be more assertive this unit, I tried to voice all my opinions in all the different labs we had to do, and while voicing them, I listened to others and I compromised with them. Hopefully in the future, I will get even more assertive.
 

Geologic Timeline Reflection

In this project, we made a timeline of Earth's history to better understand when and how some major events happened on our planet. We used a strip 10 meters long to represent the 4.6 billion years of Earth's history, where 1 million years was represented by 2 mm. One very significant major event is the creation of Earth itself, which happened 4.6 billion years ago. Nothing as we know it would exist if this collision did not happen to form our planet. The increase of oxygen in the atmosphere and organisms which use oxygen for life processes which happened in the Ordovician is an important event in Earth's history. This laid the foundation for processes such as photosynthesis and respiration, which are essential. The majority of organisms today are descended from these first organisms. The extinction of the dinosaurs was a very significant event in Earth's history as well. It happened during the Mesozoic Era and gave way for mammals to dominate. This paved a way for humans and other mammals to come into existence because the dinosaurs were very dominant at the time and the smaller mammals stood no chance.

In our scale, 1 million years was represented by 2 mm. It was surprising for how much of Earth's history there was no life. Being able to see this visually represented really put so much of history into perspective for me. Before doing this timeline, I knew that the Precambrian Era was 88% of Earth's history but when we scaled our timeline accordingly, I began to really understand how significant a part of history this is, and how we are not the biggest thing out there. We are an eye's blink compared to the history of the Earth.

Humans have made up such a small part of Earth's history, and it is surprising how much they have changed the planet in such an relatively insignificant amount of time. Humans are now the dominant species, but have been around for not even a speck in terms of geologic time.

One question I have is, how significantly have humans changed the planet in the relatively small time that they have lived on it it?

Hunger Games Final Analysis

1. In this Hunger Games Lab, we ate corks using different methods including wrist, thumb/index finger, and middle finger/index finger knuckles. Those with less food died off. Those who survived mated and tossed coins to simulate sex. The offspring was given the traits. As each generation progressed, the allele frequency changed. This stimulated natural selection and a real world population of organisms trying to survive.
2. The phenotype that was the best at capturing food was the pincher phenotype. This was because the pinchers could get the corks the easiest because using your fingers is easier than using your knuckles and wrists.  
3. Our population did evolve, according to the defintition of evolution. This is because our allele frequency changed over time. The allele frequency changed from 52-48 to 31-69 to 42-58 to 39-61 to 32-68 to 27-73 40-60 from the ration A-a. This change meant that the genotype aa was more favorable, leading more of us to try and get this genotype.
4. The non-random was the equal allele frequency at the beginning. This would help us understand the drastic change more. The non-random part were the people who retained the phenotypes. For example, if a person with big jackets and big pockets were to particiapte in this lab, he/she would do better than most, no matter their phenotype. In addition, the food was scattered randomly. Some people were farther away, and some were very close. Lastly, the physical attributes of the participants also affected the outcome. Those who are larger can scoop the food and get the food in large volumes. Those who are faster can get to the jackpot or the big pile in the middle faster.
5. If the food were larger, then the pinchers would have a more difficult time, but the stumpies would actually thrive. However, the knucklers would die first If the food were smaller, then the stumpies would die off quite fast, but the pinchers would still thrive. The knucklers would have some difficulty, but would still survive. This may be found in nature if humans intervene with nature. Some small fish in the ocean may die becuase of toxic waters, whilst big fish survive.
6. If there were no incomplete dominance, then knucklers would not exist. However, the stumpys would be much more dominant, with the allele frequency being more drastic. 
7. Natural selection is the catalyst and the driving force behind evolution. Those with favorable traits are naturally selected, and the next generation begins to look like the winners.
8. Some strategies that individuals took were to mate with those with better phenotypes or those with the same phenotype. This made it so that most offspring were pinchers and knucklers. This was natural selection, becuase those with unfavorable traits cannot mate. You cannot mate if you are dead. 
9. In evolution, an individual does not evolve. Instead, the general population evolves. Natural selection acts upon both phenotype and the genotype. The new generation's genotype consists of the dominant allele and the majority of phenotypes is the dominante phenotype. In this case, it would be the pinchers,
10. My only question is if this stimulation continued for many trials, will the allele frequency ever reach a limit?

Bird Beak Lab

Hypothesis(claim)	Evidence of this occurring	Reasoning for this
Individuals with better traits leave more offspring	Tweezer beaks had more offspring Had 44% of the total offspring	The tweezers collected more food, which made more offspring
Populations begin to look more like the winners	Almost half of the new population(44%) had tweezer  beaks	Tweezers pass on their traits and make more offspring and others don’t

 In this lab we asked the question, "If natural selection occurs in a population, how do changes in selective pressures affect the evolution of that species?" Before the environment changed, we found that out of the beak types: scissors, tweezers, scissors, and a binder clip, the tweezers got the most food resulting in more offspring.The tweezers managed to pick up enough food to support 31 chicks. The next beak type that was also quite effective was the binder clip, at 19 chicks.  The worst one out of the 4, was the spoon, at 10 chicks. This confirmed Charles Darwin's conclusion that, "Individuals whose inherited  traits help them survive and reproduce more tend to leave more offspring than other individuals." However, the environment later changed, and the results were drastically different. The environment change was that we had 10 seconds to collect food instead of 30. Here, the binder clip had the most total offspring, at 16. Tweezers were close behind, at 14 chicks. The least number of chicks was different this time. It was the scissors beak, at 7 chicks. This proves that environment changes affect a population and its traits.

While our hypothesis was supported by our data, there could have been errors due to the "food" we were given. Maybe if one beak that did not get as much offspring could have had a food that they were good at collecting. However, there might not have been as much of that food. This would have caused the beak to not produce as much offspring. Next time, make sure that all the materials that are needed are present to provide the most exact data. Secondly, it would be unfair for certain players/birds because the food would be more towards others, and also because of the limited space it didn't allow us do our best. This cause some people to maybe have an a vantage because the food was closer to them. For future references,maybe make the field a bit bigger so that it is evenly spread out.

This lab was done to demonstrate natural selection and resembles the competition between the different organisms in an environment. From this lab, I learned how different features affect the lives of species. Also, this supported conclusions of Charles Darwin. This can be used to raise awareness to protect other species from these environment changes. Based on my experience from this lab, I now get a closer feeling of the competition between animals.


 

Unit 6 Reflection

This unit focused on biotechnology, which is the use and manipulation of living things and their parts for human benefit. There are 4 main applications of biotech: industrial and environmental, agricultural, medical/ pharmaceutical, and diagnostic research. In the industrial and environmental field, there is fermentation as well as biofuels (using cellulase to break down cellulose into simple sugars as well as fermentation to produce alcohol for the fuel). Medical and pharmaceutical biotechnology includes gene therapy. Gene therapy is inserting a copy of a healthy gene into a person who has a defective copy of that gene. An example of agricultural biotechnology is classical breeding, where individuals with a certain desired trait are bred several times. GMO, or transgenic organisms, have had recombinant DNA inserted into them. I felt that I understood this overview of biotechnology fairly well. There are also certain ethical questions that are asked of the field of biotechnology, called bioethical questions. Bioethics is the study of decision-making as it applies to certain advances in biology and medicine.

One technology in the field of biotech is recombinant DNA (rDNA). It is taking DNA from one organism and inserting it into another. The first step in this is to identify the gene of interest and the location and the sequence. Restriction enzymes are very specific enzymes which cut DNA whenever they read a specific sequence. They make a jagged cut and create two "sticky ends" that can bond with other DNA. Plasmids, which are circular DNA in bacteria, are naturally resistant to a certain antibiotic. I felt that this topic was one of my strengths, especially after doing the Recombinant DNA Lab, where we modeled inserting the insulin gene into a plasmid that was resistant to tetracycline, and only the bacteria with the plasmid would survive.

Model of recombinant plasmid

Another technology of biotech is PCR (Polymerase Chain Reaction), which is a procedure that creates millions of copies of a sequence of DNA so that that sequence can be analyzed. The DNA is denatured with heat, primers are annealed to the single-stranded DNA above and below the gene, DNA Polymerase are extended, and the process is repeated. Gel electrophoresis uses electricity to separate DNA fragments based on size, since the larger fragments travel more slowly than the smaller fragments. 

In the pGLO Lab , we added a plasmid which contained GFP (Glowing Fluorescent Protein) to E.coli. There were 4 plates: -pGLO LB, -pGLO LB/amp, +pGLO LB/amp, and +pGLO amp/ara. The bacteria on the -pGLO plate formed a carpet of colonies. The -pGLO LB/amp plate had no growth. The +pGLO LB/amp plate had roughly 130 colonies, and the +pGLO LB/amp/ara had 150 colonies and glowed green under UV light. This lab helped me understand the process We also did the Candy Electrophoresis Lab, where we put four reference dyes (Blue 1, Red 40, Yellow 6, Yellow 5) into four wells. Then we extracted dyes off of candies, such as purple skittles, blue m&m's, red skittles...etc and inserted them into remaining wells. We were able to compare the size of the fragments and identify if any of the reference dyes were present in the candies. From this lab, I was able to better understand how gel electrophoresis works and how to analyze the results. 

Candy Electrophoresis Lab 

I want to learn more about gene therapy and the advances in this technology that are being made today that are getting us closer to the "GATTACA" world. I also wonder about the ethical questions that go along with so many of these advances in gene therapy. 

This year, one of my new year's goals was to actively study for tests in biology. And so far, I have done exactly that. I have studies a few weeks ahead of time, made note cards, and I studied what I had difficulty with first. This has really hepled me prepare for this test, and I will continue doing so!

PGLO Lab

 

pGLO Observations , Data Recording & Analysis

1.

Obtain your team plates.  Observe your set of  “+pGLO” plates under room light and with UV light.  Record numbers of colonies and color of colonies. Fill in the table below. Plate Number of Colonies Color of colonies under room light Color of colonies under   UV light - pGLO LB lawn yellow yellowish white - pGLO LB/amp 0 NA NA + pGLO LB/amp 62 yellow white + pGLO LB/amp/ara 350 yelow green

2.	What two new traits do your transformed bacteria have?
	The resistance to ampicillin and the GFP gene were the new traits our transformed bacteria had.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	Each colony started with 1 bacteria. There would have been between 62 and millions of bacteria first. This is because 62 was the least number of colonies and it could have gone up to millions.
4.	What is the role of arabinose in the plates?
	The role of arabinose is to make the bacteria glow green by letting the RNA Polymerase through to the gene.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	The GFP is used because of its ability to generate a glowing color. GFP is used as a active indicator for protease action because then the scientists would know that it is working. Another reason why GFP is used is because it can glow inside an organism so the scientists could see what goes on inside the organisms cell. The third use is GFP is used for Biosensors, which allows you to analyze different conditions, like pH levels.
6.	Give an example of another application of genetic engineering.

In medicine, genetic engineering has been used to mass produce human growth hormones, insulin, monoclonal antibodies, vaccines and many more.