Hunger Games Lab

1. In this lab, we simulated a real world population of organisms trying to survive. All of us split into 3 phenotypes, each of us had 3 pennies labeled front and back based on 3 genotypes (AA, Aa, aa). There were 50 - 100 pieces of food and we were given trials of 30 seconds of feeding to collect as much food as we could through the method we were given (our phenotype: Stumpys, can only pick up food with wrists, Knucklers, can only pick up food between the second knuckles of index and middle fingers, and Pinchers, can only pick up food between thumb and index finger). No more than half of us could survive, we were eliminated by the number of food we collected. Those dead would move to the perimeter and the survivors would find a mate. They would choose a mate that they think would be good at getting food, and then they would each flip a coin to determine the genotype of the offspring. The dead people would then come in to represent the new generation and the different type of species (Knucklers, Stumpys, and Pinchers). All of us would then record the number of each genotype. This whole cycle would then repeat 7 more times.

2. The phenotype that was the best at capturing food were the Pinchers due to their phenotype being an advantage over the other species. The Pinchers got to pick up the food through their thumb and index finger, which compared to the other phenotypes was the easiest way to pick up food quickly.

3. The population did evolve because in the first trial the population size was 23, having 8 Stumpys, 8 Knucklers, and 7 Pinchers, but than in the last trial the population size was down to 15, having 0 Stumpys, 9 Knucklers, and 6 Pinchers. This shows how the overall population size decreased, meaning that the population did in fact evolve.

4. In this lab, the things that were random were how the food was placed on the field. Sometimes it was all evenly spread out, sometimes there were more at one part of the field, and other times it was all piled up in the center. This affected the evolution of the population because if there was more on part of the field than whichever species that were closest to the food would perspire. And if it was all evenly spread out or it was all piled up in the center, whichever species that was the fastest and had the most advantageous phenotype would live on and give birth to offspring.

5. The results would have been definitely different if the food was larger or smaller. If the food was larger than it could've been harder to collect so the species would've been unable to collect enough food and the population would decrease. If the food was smaller than it could've been easier to collect so species would be able to pick up food more easily which could lead to the population rising.

6. If there was no incomplete dominance then the results would've been different because in this case, if there were 0 Knucklers, than the Stumpys would die, resulting in Pinchers being able to collect the most food. If the Pinchers collect the most food than they'll have offspring but the offspring will have to go against each other for food since all the other species have already died out, which is harder thus the population decreasing.

7. Evolution is the result of natural selection. Natural selection eliminates species with worse traits and give species with better traits the chance to expand their population through offspring and this leads to evolution because once this process happens the population begins to look more like winners; and evolution is the change in allele frequency over time.

8. Strategies that group of people adopt in order to increase their likelihood of survival and reproduction is that species of the same kind would work together and team up in order to have their specific population size increase, as well as survive. This would result in their specific allele frequency in the population to increase. In nature, this is also what happens, species of the same kind team up together in order to beat other species so that the species themselves can survive and reproduce.

9. In evolution, the whole population size evolves due to natural selection. Natural selection acts on both genotype and phenotype since it changes both the appearance and genetic makeup of an animal over time. When the process of natural selection happens. those with better phenotype, caused by the genotype, survive and reproduce, looking like the winners of a population.

- A question I still have is how would the world have been like if there was no natural selection, thus evolution. Would every species just keep staying the same since none are changing?


Graph:

Bird Beak Lab

1.Graphs:

Part 1 Analysis:

Claim/hypothesis: 

"Individual with better traits leave more offspring."

 My group and I did a experiment using different kind of utensils, that resembled and represented different kinds of beak of birds, to test which beak would collect the most "food" (Macaroni "seeds", Paper clips "seeds", Rubber bands "leaves", and Toothpicks "seed pods"), thus have more offspring. We had three different trials and in the end we got our results. The tweezers beak bird had a total of 25 chicks, the scissors beak bird 14, the binder clip beak bird 18, and the spoon beak bird 9. This supports the claim because it shows how individuals with better traits, in this case the tweezers beak bird and binder clip beak bird, do produce more offspring than individuals with worse traits, the scissor beak bird and the spoon beak bird. The tweezers beak bird and binder clip bird would produce more offspring than the scissor beak bird and the spoon beak bird because they collect more food, with the help of their better traits, which means that they could have more chicks to feed that extra amount of food to. 

"Populations begin to look more like the winners."

From the experiment described in the first CER paragraph, we collected data showing how out of 100% (the population), from the order of individuals with better traits (the winners) to ones with worse traits (the losers), the percentage of chicks in the population from the different beak birds were: the tweezers beak bird boasting 37.9%, the binder clip beak bird with 27.3%, the scissor beak bird with 21.2%, and lastly, the spoon beak bird with only 13.6%. This supports the claim that populations begin to look more like the winners because it shows how out of the whole population (100%) the birds that covered it more were the birds that had won (have better traits, therefore collect more food, thus have more offspring), in this case the tweezers beak bird and the binder clip beak bird, each covering more than 1/4 of the population. 

Part 2 Conclusion:

The question of this lab was: "If natural selection occurs in a population, how do changes in selective pressures affect the evolution of that species?" To that question, my hypothesis is: If a famine hits in the area and in order to survive there needs to be 10 items of food for each offspring, then there will be less offspring overall. My group and I carried out the experiment again, getting new results. Overall there were less offspring, this time instead of having a total of 66 offspring like how before the famine hit, there were only 29 chicks. This supports my claim of there being less offspring overall because my evidence shows how the number of chicks decreased drastically, lessening more than half. The number of chicks overall probably decreased so much because the amount of food needed in order to survive increased and this makes the competition between the different beak birds harder, thus the result of less chicks for each bird (since there is now technically less food for every bird).

An error that could've occur in this lab is the miscount of rubber band "leaves" for the scissors beak bird due to them cutting some of the bands in half (or even more), resulting in them having twice (or more) the actual "leaves" they have. To minimize this error, thicker rubber bands can be used, making it harder for the scissors beak to accidentally cut them. A second error that could've occur in this lab is miscounting of the amount of food. Anyone could've easily accidentally skipped a number or two when counting their amount of food and this could've have lead to them writing down that they have more chicks than they actually do. To minimize this error, when doing this process students can slowly and quietly (in order to not be a distraction to others also counting) count two times, in order to make sure that their number's correct.

The purpose of this lab is to help us understand what Mr.Orre taught us in the vodcasts: Darwin's 4 observations and how natural selection causes evolution. Natural selection causing evolution occurs everywhere in our lives constantly, including in our own human race. As each generation of humans pass by, it is said that we get more and more attractive overall. This is so because those already attractive attract others that are also attractive, leading to them both mating and birthing a child that have their attractive traits.

Unit 7 Reflection

In this unit, we learned about Ecology, the study of interactions between organisms and their environment, and its' basics: the idea of Homeostasis/Equilibrium, which is that like the body environments are healthiest when they're in balance, and the idea of Interdependence, when all living things are dependent on each other, and abiotic(nonliving) factors for survival. In a ecosystem, there are habitats and their niches, which includes all factors that species need to survive, stay healthy, and reproduce. We also went through the different Levels of Organization on Earth: Organism,  an individual living thing, Population, group of the same species that live in 1 area, Community, group of different species that live together in 1 area, Ecoystem, includes all abiotic and biotic factors, and the Biome/Biosphere, which is a large are of the world that's made of several ecosystems. In this world, animals, called Consumers aka Heterotrophs, compete with each other for food/energy(except for Producers/Autotrophs), Food Chains and Food Webs show this. Food Chains show how each organisms gets its energy; in the chain, the arrow points to the one getting energy. There are different levels in a Food Chain, called Trophic levels, that are based on what something eats. The 5 Trophic levels are (from lowest to highest): Primary Producer, Primary Consumer, Secondary Consumer, Tertiary Consumer, and Quaternary Consumer. There are not only different level Consumers, there are also different type of Consumers: Herbivores(plant eaters), Carnivores(meat eaters), Omnivore(everything eaters), and Detritivore/Decomposers (dead/decaying eaters). In comparison to Food Chains, Food Webs are more accurate and most of the animals in Food Webs eat more than 1 thing. Relating to Ecosystem Energy, we also learned about the transfer of Energy. We learned the Unit of Energy: Biomass, which is a method of measuring energy and is the total dry mass (weight) of organisms in a given area. Biomass is measured in calories (or Joules) and it's without water because water has no energy. The energy is stored in bands of cellulose; as consumers eat, they transform energy, passing on only 10% to the next level. Very little stays in the organism, 90% is lost as waste (such as heat). Energy being transformed is shown through Energy Pyramids. There is also the Population Pyramid which shows the effect of the 10% Rule: If only 10% of energy is passed on, less and less energy is available for top level consumers. This results in having fewer consumers and smaller populations at higher levels. Coming from the Population Pyramid, Population Ecology, the study of population relation to the environment, was also went through. It includes density, the # of individuals per unit area/volume, and dispersion, the pattern of spacing through individuals within bounds boundaries of population. There are also certain factors that affect population, including immigration, influence of new individuals from other areas, and emigration, which is movement leaving. Births and Deaths are also large factors that affect the population. There's also Exponential Growth, when there's lots of growth over a short time, which is something we humans are going through. In Ecosystem recycling, there is Succession, three types: Ecological succession, the sequence  of community and ecosystem changes after a disturbance, Primary succession, when succession begins with no soil to start with, and Secondary succession, which begins in an area where soil remains after a disturbance. In Succession, there's an order: it begins with Pioneer species to Intermediate species than finally to the Climax community. In an Ecosystem, the producers are critical, but they're also limited by the amount of nutrients they have. No nutrients mean no energy produced. And if there's no producers, then there's no carbon energy for life. Alongside with producers, decomposers are also critical. The four nutrients are Water, Carbon, Nitrogen, Phosphorous and without their cycles there wouldn't be any in the atmosphere. There's also the health of an Ecosystem, which includes it's loss (endangered/threatened species, mass extinctions, etc.) , it's gains (emigration, introduced/exotic species, etc),  and over exploitation and change in climate. Last and not least, we also learned how we could help the planet be better, by identifying the problem(s), solving/reducing the problem(s), and spreading awareness to everyone.

I don't think I have any unanswered questions but I would like to learn more about the different types of succession and I would like to see more examples regarding them. I wonder when our planet will become a disastrous place that we can no longer survive in and how it became to be that (if it was because of us).

The Conservation Biologist Project actually went better than I thought it was going to go. A lot of things went well: all my team members cooperated, we each completed our parts in time, and we each tried to help each other out as much as possible. There were barely, if not any, arguing and I think the collaboration went really well. I sincerely think that we all did a good job and nothing really went badly, except for some technical issues at the end. I didn't really learn anything, I think the main reason why the collaboration was so good was because we each were willing to put in as much effort as we can in this project. Through the self assessment test, I found out that my dominant conflict style is aggressiveness. When people are rude or sarcastic toward me, I tend to do it back. I also consider myself pretty heated since little things can easily aggravate me. I'm also super short-tempered and snappy when I'm under stress. In order to be more assertive, I need to be more direct and stop letting things I disagree with pass and let my voice be heard.

Unit 6 Reflection

In this unit, something we learned about was Biotechnology, the study and manipulation of livings things in order to benefit mankind, and how it applies to our lives. We learned that it was a large field that usually focuses on understanding of DNA, proteins, and inheritance. With these understandings, were its' 4 applications: Industrial and Environmental Biotechnology (ex: fermentation for food/beverages, biofuels, etc.), Agriculture Biotechnology (ex: Breeding of plants/animals, transgenic organisms, aquaculture), Medical/ Pharmaceutical Biotechnology (ex: medicines from plants. fungi. animals, etc.), and Diagnostic Research Biotechnology (ex: DNA identification for crime scenes and the compare and contrast of DNA for organisms). When learning about these applications and how they take place in my life I realized that they are constantly a part of my life, whether it's the medicine I take from plants or the GMO fruits that I eat. With Biotechnology comes Bioethics, the study of decision-making as it applies to moral decisions that have to be made due to advances in biology (such as biotechnology), medicine, and technology. We learned about the factors involved in making a bioethical decision: our moral (a conviction position, having to do with weather something is considered right or wrong) and our values ( what we see as important or moral; everyone's values are DIFFERENT). There are also steps to making a bioethical decision: how before deciding anything in Biotechnology you should identify the problem, think out the pros and cons, and so on so forth. Really, it's a lot like making a normal important decision. Another kind of technology we learned about was Recombinant DNA technology, rDNA, which is the insertion of DNA of one organism into the DNA of another. This is often described as genetic engineering. There are certain tools needed in order for this process to happen: the gene of interest, restriction enzymes (they cut the DNA if they read the specific sequence), plasmids, which contains the replication gene that tells the plasmid to be copied and has antibiotic resistance,  and ligase, the enzyme that finishes it all off by reattaching the base pairs. We also got familiar with the technologies of Biotechnology: Polymerase Chain Reaction (PCR), a procedure that yields millions of copies of a sequence of DNA, Gel Electrophoresis, using electricity to separate DNA fragments of known lengths, and Sequencing, the determination of the exact sequence, or order, of a given DNA strand using DNA polymerase, primers, extra bases, and florescent dyes. The last essential understanding to this unit was Bacterial Transformation, the process by which bacterial cells take up naked DNA molecules, and how we can use green fluorescent protein to identify the number of bacterial colonies, due to its' glowing under a UV light because of the arabonose that activates the gene. 

I'm proud to say that in this unit, for the most part, I understood what was going on and the concepts. Because of the emphasis we put on Gel Electrophoresis, I feel as if I have a true understanding for it and believe that it could be one of my strongest strengths in this unit. Another one of my strengths was Bioethics, since for that you only really needed logic to understand it, and Biotechnology and it's applications since I realized how much of a part it plays in my life. I also really understood rDNA and the restriction enzymes because of the lab we did in class, it really demonstrated the process and I feel pretty comfortable with the concept. Along with my strengths were my weaknesses. I had a hard time understanding the connection of Bacterial Transformation and pGLO. I don't fully understand how they relate and I don't really understand what happened in the pGLO lab. I also don't really understand what sequencing is and why it's an essential understanding in this unit since I feel as if we didn't really go over it since we mostly focused on Gel Electrophoresis. 

The labs that we did in this unit were the "Thinking Like a Biotechnican" lab http://lkbiologyblog.blogspot.com/2016/01/thinking-like-biotechnician.html , in which we made models of recombinant DNA,

the Candy Electrophoresis lab http://lkbiologyblog.blogspot.com/2016/01/candy-electrophoresis-lab.html , in which we got familiar with the process of Gel Electrophoresis, and the pGLO lab http://lkbiologyblog.blogspot.com/2016/01/pglo-lab.html , in which we transformed bacteria. From this, I've developed a deeper understanding about rDNA and its' tools and the process of Gel Electrophoresis, 

I would like to learn more about my unanswered questions: sequencing, since I can barely grasp what it is and I feel like we didn't go over it a lot, and Bacterial Transformation and it's connection to what we did in the pGLO lab. I wonder what these concepts are and I wonder if they are important in our lives and if so then how.

My goal to get a better grade in Biology this semester is slowly moving along. I think I've been making improvements and I'm very proud of them. So far I've been turning all my assignments in in time, except for the one previous virtual lab, and I've been really understanding how what's talked about in the vodcasts relate to what we do in the labs, other then the pGLO lab. Even though I'm slowly getting better, I still have a lot of things to work on. I haven't started reading ahead in the textbook and I'm still procrastinating a lot, even though I'm better at not procrastinating than before now. Procrastination has always been a bad habit for me so it's very hard to break now. My next steps regarding this goal will be to keep on turning assignments in in time, to continue observing the connection of the vodcasts and the labs, to start reading ahead in the textbook, and to fight the urge to procrastinate even harder. My second goal, to have a better sleep schedule, has been a complete wreck. My sleeping schedule right now is all over the place due to the fact that I still procrastinate too much, which leads to me staying up late at night or even pulling an all nighter, and that I take long naps during the day after school and only wake up at 9 PM or later. For this goal, my next steps will be to definitely stop procrastinating so much, that it leads to restless nights, and to stop taking such long naps after school. 

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 carpet Yellowish Tan Greenish Blue - pGLO LB/amp none + pGLO LB/amp 164 Yellowish Tan Greenish Blue + pGLO LB/amp/ara 59 Yellowish Tan Greenish Blue

2.	What two new traits do your transformed bacteria have?
	Two new traits my transformed bacteria have are ampicillin resistance and arabinose.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	There were probably only one or two colonies of bacteria in the 100 uL of bacteria that was spread on each plate because when we got the bacteria with the lobe we only got a tiny amount of it.
4.	What is the role of arabinose in the plates?
	The role of arabinose in the plates was to activate the gene so that it could glow.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	In cellular biology, GFP has been used as: Reporter Gene (a gene that researchers attach to a regulatory sequence of another gene of interest in bacteria cell culture, animals or plants) Cell Maker Fusion Tag (a protein or a peptide located either on the C- or N- terminal of the target protein)
6.	Give an example of another application of genetic engineering.

Genetic engineering is also used in agriculture to create genetically-modified crops or genetically-modified organisms.

Candy Electrophoresis Lab

1) When analyzing the results of my gel, none of my experimental samples contained dyes that did not match the four reference dyes. There were no dye bands that were a different size than any of the reference bands, no dyes that were a complete different color than any of the reference bands, no more than one color band, and no dyes that were moving in the “wrong” direction. Both of the blue samples matched with the blue reference dye as moving the slowest, meaning they're also the longest strands. The yellow, orange, and red reference samples and dyes all traveled the same length in the gel. 2) Out of the four structures of the dyes pictured (Carminic acid, Betanin (beetroot red), Fast green FCF, and Citrus red 2), the dyes that would migrate similarly to the dyes I examined in this lab would be Citrus red 2 for the red, yellow, orange dyes and Betanin for the blue dye. Citrus red 2 would migrate similarly to the red, yellow, orange dyes because all their structures are alike, short, which means that they would all travel quickly. Betanin would migrate similarly to the blue dye because both their structures are alike, long(est), which would make them move slowly. 3) Dog food manufacturers put artificial food colors in dog food in order to make it look more appealing and "better" (tastier, healthier) to the the owners of the dog that are buying the food. 5) Two factors that control the distance the colored dye solutions migrate are the length (longer = travel more slowly; shorter = travel faster) and charge of the dyes. 6) The force that helps move the dyes through the gel is electricity. 7) The component of the electrophoresis system that causes the molecules to separate by size are the gel lanes and the electric current that runs through the gel because it's what causes how fast short structured dyes move and how slow long structured dyes move. 8) DNA molecules with molecular weights of 600, 1000, 2000, and 5000 Daltons would separate in this order: The DNA molecule weighing 600 would be the first one ahead (furthest from the wells), since it weights the least thus would be quickest, the 1000 Dalton DNA molecule would follow behind, which would also have the 2000 Dalton DNA molecule behind it, and lastly would be the 5000 Dalton DNA molecule (closest to the wells), since it weights the heaviest and thus would be the slowest.

Thinking Like a Biotechnician

Recombinant DNA, the process of the insertion of one organism's DNA into the DNA of another, requires a transformation. Restriction enzymes, bacterial enzymes that are major tools of recombinant DNA technology, recognizes a specific nucleotide sequence in DNA molecules, and cuts the backbones of the molecules at that sequence. In this experiment, the restriction enzyme I used was Eco RI because it made cuts close to the insulin gene, on both sides, and it could cut the plasmid and cell DNA. In this experiment, I chose a restriction enzyme that cut the plasmid in only one place but if it had cut the plasmid in two different places than the result would not be not just one fragment of DNA, but two fragments of DNA. After the restriction enzyme does its work, there then is a set of double-stranded DNA fragment with "sticky ends", single stranded ends. The bases of these single stranded ends easily form base pairs with the complementary bases on other DNA molecules. Therefore, these ends can be used to join DNA pieces that are from different sources. Using plasmids, small circular pieces of DNA found in bacteria, the recombinant DNA molecules can be made to replicate and function genetically within a cell. Small DNA fragments are inserted into the plasmids, then introduced into bacterial cells. As the bacteria reproduces, so do the recombinant plasmids, resulting a bacterial colony in which the foreign gene has been cloned. The antibiotic I would use in my petri dishes to see if bacteria have taken in my plasmid is kanamycin because it's the one that the plasmid had resistance to, which would help me identify the bacteria that had taken in my plasmid because the bacteria that hadn't would all be killed off. Anitbiotics that I wouldn't use would be tetracycline and ampicillin because the plasmid didn't have resistance to it, which wouldn't help me identify the bacteria that had taken in my plasmid because there would be none since all of them had been killed off. This technology could be important in everyday life because it lets us insert new genes into already there genes, which could be programmed to benefit us by making organisms/plants better or (more) beneficial to us. Some real life examples of this technology being used are pest resistant crops, vaccines, and transgenic animals.