Bird Beak Lab

For part 1, I hypothesized that the tweezer beak would do extremely well because it can eat a lot of food very quickly. My hypothesis was confirmed when 40% of the bird chicks had tweezer beaks. However, I overestimated how well the tweezers would do, because the binder clip came in for a close 2nd place at 33%. Because 40% of the second generation had tweezer beaks, my claim that tweezer beaks were a very useful trait is correct.

I also hypothesized that the entire population would have tweezer beaks. This did not happen over the span of 3 years that we tested, as only 40% of the chicks received tweezer beaks. However, the trend indicates that over a longer period time, the majority of the birds would have tweezer beaks and the other alleles would only be passed on through heterozygous birds. The current evidence proves my hypothesis incorrect, but a more precise and longer experiment may support my claim.

Percentage of chicks w/ each Beak (before environmental change)

When a drought occurred and wiped out all of the seed pod plants (toothpicks), I made the claim that the scissor beaked birds may not do as well due to their reliance on the seed pods. The percentage of chicks with scissor beaks decreased by 1%, indicating the scissor beaks weren't as favorable. But the percentage is definitely within the margin of error, meaning the drought made no significant difference for the scissor beaked birds. The binder clip beaked birds made 1% less chicks as well and the spoon beaked birds made 2% more chicks. Because these changes are also within the experiment's margin of error, the seed pods weren't an important food source in the ecosystem. My hypothesis is not supported by the data, but more accurate experimentation should corroborate my claim.

One error that I am pretty sure occurred is that each person has a different skill level at picking up the food. Because some people may be better at picking up the pieces than others, the results may show something that is dependent on skill rather than beak type. To fix this problem, I would rotate the beak types to each person in the table so that everyone has 3 years with each beak type. They would then find the numbers for each beak at the end of 3 years and average them out. This would make it so that every beak's numbers are altered in the same way by each person, resulting in data that isn't influenced by a group member's skill. I also think it would be more accurate if each beak type was more specialized and dependent on a single food type. For example, the scissor beaks were supposed to be affected by the absence of toothpicks, but they survived perfectly fine. Instead of scissor beaks and toothpicks, maybe it could have been done with a magnetic beak dependent on paper clips. If the paper clips were removed, it would have a much more visible effect on the birds with magnetic beaks.

The purpose of this lab was to see how environmental changes can affect the allele frequency of a population. This relates to what we have already learned because the vodcasts talked about favorable mutations and how environmental pressures select certain traits. This selection can cause a large change in the population over time. Our experiment was quite flawed because there was no real change in part 2. However, I now can apply my knowledge of incorrect experiment execution to other contexts. This is because I now know that variation in skill level can overshadow the result the experiment is trying to get to.

Percentage of chicks w/ each Beak (after environmental change)

Ban Plastic Microbeads! (Story of Stuff Extra Credit Summary and Reflection)

The Story of Stuff video I watched was about banning plastic microbeads that take forever to decompose and are virtually impossible to clean up. Basically, companies put these microscopic pieces of plastic into cosmetics and toiletries because consumers find their texture satisfying. And because the microbeads are so small, they can’t be filtered out of the water at treatment plants. This results in the plastic ending up in the ocean, where fish and other animals mistakenly eat it, thinking that the beads are plankton. The beads also act “as a sponge for toxins” and concentrate poisonous substances that are harmful to living things. As the microbeads travel up the trophic pyramid and reach us, biomagnification occurs causing fish that we eat to have high levels of plastics and toxins.

Again, due to their small size, cleaning up is virtually impossible so prevention is the only solution. In numerous states including California, legislators are currently in the midst of passing laws that would ban the sale of products with microbeads. This doesn’t mean we won’t be able to use shampoo anymore, it just means that companies will be forced to switch to more environmentally friendly exfoliants if they want to continue selling to the 40 million people who live here.

I really liked this video because it explained what microbeads are, what their effect is, and what the solutions are, in an organized and interesting manner. They used really nice animations and were successful at portraying the large corporations as what they are: people who only care about money. However, it would have been nice if they went more into depth about topics like biomagnification and what brand lines to avoid.

I already check labels of shampoo and soap for things like parabens, pthalates, SLS and other possible carcinogens. Now I know to also look for things that are obviously plastic like polyethylene, polypropylene, and polymethyl methacrylate. By doing this, I will be voting with my dollar for environmentally friendly products. I will also feel more safe because who knows what kind of havoc plastic will wreak when it enters your body.

Watch the video here

Take action here

Watch another video about microplastics here

Unit 7 Reflection

This unit was about ecological principles and how humans affect the environment. We learned about population ecology and how all the species in an ecosystem are dependent on one another. We also focused on how energy moves through trophic levels and explored ideas like the 10% rule and how the collapse of one level can topple the rest of the pyramid. There were many videos that were shown, such as "Bag It!", relating to how we can help save the environment and reduce human created issues like plastic in oceans.

I want to learn more about how the government interacts with the environment and how passing laws could help reduce climate change. I also want to learn about how we can increase social awareness of environmental issues and galvanize the masses into making change.

I think the Conservation Biology Project was really fun and I hope we will have similar projects in the future. It took us quite a while to decide on our topic and I was a bit aggressive in convincing my partners to go with my idea. However, we were able to assign work well and get all the notes organized into one document. We then wrote the script using ideas from the notes, but I feel like we didn't divide up the script work that well so I ended up typing most of the document. After filming a Bill-Nye style video during class, we had a number of surprises after school. Chloe discovered that some of the clips were missing, so I needed to record voice-overs and create a couple images to show while I was talking. Also, when we checked the instructions on Canvas, I noticed that we were completely missing some information. To fix this, I wrote a new portion of the script and filmed myself speaking it. Chloe then finished off the editing while Kaitlyn and I did the image citations. Overall, this project was great and because I work well under stress and late at night, I ended up finding the last-minute work quite enjoyable.

Our Conservation Biologist Project was about invasive comb jellies (Mnemiopsis Leidyi pictured above)

The survey showed that my dominant conflict style is assertive, but aggressive comes in as a close second. Although I'm already really assertive, I think I need to be less aggressive when debating with others. To combat this, I can be more conscious of what I'm saying and ensure that what I'm saying really is contributing to the conversation rather than just making the other person feel bad. I should also be more receptive to other's ideas. I actually have made the conscious effort in the past few weeks to accept other people's ideas as valid as mine. I will need to continue this behavior and put more effort into thinking about my words if I want to reduce my aggressiveness in conversation.

Unit 6 Reflection

In this unit we learned about biotechnology and genetic modification. Biotechnology is divided into four fields: agricultural, industrial, medical, and forensics. Because humans can now modify organisms in so many ways, we also learned how to make ethical decisions on biotechnological topics. To make an ethical decision, you must first understand the choices and list pros and cons. Then find a decision that fits your morals most. The core of this unit was with recombinant DNA, electrophoresis, PCR, and DNA sequencing. Recombinant DNA is when genetic material is taken from different organisms and inserted into the DNA of a target organism. Electrophoresis allows scientists to separate DNA based on strand length. Polymerase Chain Reaction creates many copies of a strand of DNA, giving scientists the ability to examine the strands much more closely. To sequence genes, there are many possible techniques. One of them involves fluorescent dyes binding to bases depending on what base it is. Computer programs then examine the pattern of fluorescent dyes, telling the scientists what the genetic code is.

This unit had some very interesting information, although while writing this reflection I did need to go back and check on some stuff in the vodcasts. This means that I need to study from the bioethics and technologies of biotechnology vodcasts to prepare for the test.

One thing I really loved in this unit was the labs. Unlike other labs I have done in school where the results are predictable and uninteresting, the candy electrophoresis lab and pGLO lab had amazing results. In the electrophoresis lab all of our dyes matched the standard ones, but another group that extracted a green dye saw it separate into its blue and yellow parts (http://rpbioloblog.blogspot.com/2016/01/candy-electrophoresis-lab-conclusion.html). Our plate of fluorescent bacteria from the pGLO lab had one of the highest colony counts in the class and it was cool seeing the E. Coli glowing in one petri dish but not in others. (http://rpbioloblog.blogspot.com/2016/01/pglo-lab-conclusion.html)

I would love to experiment with other traits and inserting them into E. Coli bacteria. I wonder whether adding too many extra genes for protein creation will cause the bacteria to be unable to complete its basic life processes. In other words, will adding enough genes kill the bacterium.

I have failed to keep up to one of my new years goals while I have partially followed the other. At the start of the new year, I pledged to work on my textbook notes throughout the unit so I wouldn't have too much work on the day before it is due (aka today). I did not go through with this promise, probably due to the fact that I did not remind myself enough. Now on, I will set a weekly reminder on my phone to work on my textbook notes. I also said I will study 3 times a week for math to get at least 90%. Although I do not have specific study sessions, whenever I do my math homework I also go over all of my notes from that day and from the rest of the module.

Recombinant DNA where we used restriction enzymes to insert the insulin gene into a plasmid

http://rpbioloblog.blogspot.com/2016/01/recombinant-dna-lab.html

Candy electrophoresis lab where we extracted dye from candies to compare them to 4 standard dyes by using electrophoresis

http://rpbioloblog.blogspot.com/2016/01/candy-electrophoresis-lab-conclusion.html

pGLO lab where we made E. Coli bacteria absorb plasmids containing the GFP gene.

http://rpbioloblog.blogspot.com/2016/01/pglo-lab-conclusion.html

pGLO Lab Conclusion

1.

2. Our new bacteria have ampicillin resistance and they glow under ultraviolet light.

3. Since we have around 200 bacteria in our amp/ara/LB plate, and 150 in our amp/ara plate, and all of these took in the GFP gene, there must be at least 350 bacteria that took in the GFP gene. If the absorption rate is around 1 in 3, then there were probably around 1000 bacteria in the 100 microliter solution.

4. The purpose of arabinose is to activate the GFP gene and serve as a method of controlling the glow. If the arabinose is not present, bacteria will not produce GFP even if they have the gene.

5. GFP can be used to track the spread of bacteria with a certain trait. They are also an easy way to indicate whether an organism is genetically modified or not. GFP can be used to track the movements of certain cancers like osteosarcoma in dogs.

6. Another use of genetic engineering is to increase crop yield without spending large periods of time on breeding the perfect plant. Genetic engineering may be extremely important in the future with humanity's rising population and need for quick access to food.

The amp/ara/LB plate with bacteria fluorescing under UV light

Candy Electrophoresis Lab Conclusion

Although none of our dyes traveled in the wrong direction or mixed colors, there were some minor differences between the reference dyes and the ones we were testing. For example, our red and orange were darker than the reference colors, whereas the reference dyes for blue and yellow were darker than ours. However, I think this can be attributed to the amount of dye we extracted from the candy. I did not find any major variance between the distance traveled by reference and test.

I think that citrus red 2 will migrate similar to the blue 1, carminic acid will go about as far as our red 40, fast green FCF should go about as far as yellow 6, and betanin will be about the same distance as yellow 5. This is my hypothesis because although they aren't the same colors and size of molecules, the order of dyes that we tested, yellow 5, yellow 6, red, blue will correspond to betanin, fast green FCF, carminic acid, and citrus red 2. In other words, although the chemicals won't go as far as the dyes (due to their size), they should order up in the way specified above.

Dog food manufacturers probably put food coloring in the dog food to entice the dogs to eat it. Most dog food does not consist of things that a dog would naturally be fed, so to get the dog to eat up, they need to use artificial flavoring, coloring and smells.

In my food I found the artificial dyes red 40, yellow 5, yellow 6, and blue 1. I also found 2 natural dyes in cereal: annato extract color, and turmeric extract color. I found most of these dyes in cereals and sauces. It surprised me that I found the exact same dyes that we tested in the lab. I then searched the dyes up and learned that they are four of the seven permitted food colorings in the US.

The 2 factors that control the distance the dye travels is the dye's size, and how long you leave the gel in the electrophoresis box. In addition, I also think that the overall charge of the dye must also play a part in the direction it travels.

The force that moves the dye through the gel is the electromagnetic force. It is propagated through the current, caused by the voltage difference from the red cathode to the black one.

The reason why smaller dyes travel farther than large molecules of dye is because of the porous nature of the gel. Because the dye is inserted into the wells, they travel through the gel rather than on top. Thus, smaller dye molecules find it easier to navigate the cave-like environment found inside the gel.

Because DNA molecules of this size are so much larger than the dyes, I expect them not to travel as far. For this reason, it is necessary to leave the electrophoresis going for longer to see a difference in the distance traveled by each molecule of DNA.

After only a couple minutes of electrophoresis

The entire apparatus

The gel as removed. References are red-blue on left, test dyes are red-blue on right.

Recombinant DNA Lab

Process: To produce recombinant DNA, you first need a plasmid that has some antibiotic resistance. Our plasmid was resistant to ampicillin. This plasmid is cut open by a restriction enzyme which also cuts the insulin gene out of another piece of DNA. For us finding an enzyme that did all of this was quite tedious, and unfortunately, the one that worked was the last one to try.This insulin gene that was chopped out and some of its surrounding code are inserted into the plasmid and stuck together by using the enzyme ligase. This plasmid with the insulin gene and antibiotic resistance is then inserted into a bacteria. This bacteria then replicates and passes the antibiotic resistance on to all of its offspring. Ampicillin can then be added to the petri dish to kill off all the bacteria that don't have antibiotic resistance, thus leaving only the bacteria that produce insulin.

1. In my petri dish I would only use antibiotics that I know the plasmid carried resistance for. Otherwise, I might kill off the bacteria that have the insulin gene too. I also won't use antibiotics that all the bacteria in the species are resistant too, because that wouldn't refine the types of bacteria in the dish.

2. Restriction enzymes are enzymes that cut open DNA when they read a certain sequence. They work by cutting in patterns that create "sticky ends". I used HIND III because it cut extremely close to the insulin gene on both sides, as well as cut open my plasmid in one place.

3. If my enzyme cut the plasmid in 2 locations, then once the insulin gene is inserted in, I would be left with a string of DNA rather than a loop. However, I think that if ligase is introduced, the plasmid will reconnect to itself and everything would proceed as normal.

4. This process is important in our daily lives, because bacteria are extremely useful factories for protein. Although right now the only well-known use for bacteria-produced protein is insulin, I am sure in the future, we will be using bacteria as factories for all types of materials.

5. This process could eventually actually be used for bacteria to convert things like plastic and feces into usable fuel or other goods. For example, we would first have to engineer an enzyme for the digestion of plastics. We may then have to convert this into a genetic code. The code could be produced by various DNA "printer" technologies that are being innovated today. This gene will then be spliced by a restriction enzyme that also splices open a plasmid. The process will then be repeated except with an enzyme for the construction of propane or another fuel. Once all the necessary plasmids are inserted into bacteria, we could essentially feed the colony our plastic waste, and fill our cars or propane tanks out of the other side.

The plasmid with insulin gene and ampicillin resistance