Unit 8 Reflection

This unit was about evolution and how it occurs.  Evolution is a process where mutations that are favorable for an environment become more common. This happens because organisms with favorable mutations are more likely to reproduce. We know that natural selection has occurred if there is an overall shift in the allele frequency of a population.

 In this picture, a form of selection that favors one extreme of a trait over medial and the other extreme. For example, if large claws helped a lion survive, then directional selection could occur and make large claws a common trait.

Another way we can know evolution has occurred and whether two species have a common ancestor is by looking for homologous structures. These are structures like bat wings and whale fins that have different functions but came from a common ancestor's structure.

Evolution takes place over long periods of time. The earth has been around for 4.6 billion years and basic life didn't pop up until 3.8 BYA. During the Cambrian explosion, 542 MYA, most eukaryotic phylums that we are familiar with popped up. After this event, we have a mostly clear fossil record through which we can trace evolutionary paths. What is really surprising is that H. Sapiens Sapiens only evolved 200,000 years ago. This is a blink-of-an-eye ago in geologic terms, meaning that we aren't as significant as we like to think of ourselves as.

I want to learn more about the relationship between the different ways of speciation and natural selection because it is not completely clear to me yet. I'm very interested in the classification of organisms so I want to find out more about phylogenetics.

In my Unit 7 reflection, I talked about being assertive. The survey found that assertiveness is my dominant trait and aggressiveness is strong as well. In the geologic timeline project, I have been very assertive and made sure that things got done in the best & most efficient way possible.  However, I was also quite aggressive in convincing my groupmates to do what I thought was best. I was conscious of my words and actions, which allowed me to only use aggression when trying to get something done. In my next group project, I will try to be more accepting of my teammates' thoughts and ideas.

Geologic Timeline Individual Reflection

The first major event in Earth's history is its formation. The Earth formed around 4.6 billion years ago as a magma ball that was constantly being pummeled by meteors. Slowly, it cooled down and developed a carbon dioxide atmosphere that protected the surface from celestial objects. The formation is very significant because without it, there would be no place for life to develop in our solar system.
Another important event is the Great Oxygenation Event. The event occurred around 2.3 billion years ago because of the appearance of Cyanobacteria that converted carbon dioxide into oxygen. It is a vital event because it allowed aerobic organisms to evolve and all multicellular life depends on oxygen for survival.
A huge event in the history of our planet is the Industrial Revolution. The Industrial Revolution started about 200 years ago and created a shift from mostly manual, cottage-industry style companies to concentrated, urbanized factories that depended on fossil fuels for power. The event in part lead to our current global society and materialistic, unsustainable lives. If the industrial revolution didn't occur, we may not be as technologically advanced, but we also wouldn't be seeing spikes in CO2 levels, temperature fluctuations, extreme weather events, microplastics in our oceans, and colossal extinction rates.

The Earth's history stretches from 4.6 billion years ago to today. If we compressed the 13.8 billion years that the universe has existed into 365 days, all human history would take place in the last few seconds of the last day of December. Although I knew the geologic time scale very well before this, I had never come across this comparison. The comparison shows how small and insignificant we are as well as how many millions of years of evolution it has taken for us to develop.

In our short time on Earth, humans have caused extinctions, elevated CO2 levels, climate change, and plastic to become extremely common. I think that by devastating our environment, we are being unfair to both our ancestors and our descendants. We are being unfair to our ancestors by harming other species which we are actually quite closely related to and destroying the planet that they contributed so much energy to. Environmental issues are very detrimental to our descendants because they will have to live in a barren world and deal with the consequences of our materialism.

Hunger Games Lab

1. In this lab, we assigned people to certain types of feeding patterns. People with the AA genotype had to pick up food (corks) with their wrists, Aa had to use their second knuckles, and aa had to use their fingers. Each round, each individual would need to have eaten a certain amount of food to reproduce and survive. If the survive, they find a mate and flip coins to choose their baby's genotype. As the experiment goes on, favorable traits reproduce more and the allele frequency changes. The experiment simulated how natural selection occurs and put together the concepts of mendelian genetics and survival of the fittest.

2. The data shows that the knucklers were the best at capturing food. However, this is most likely a result of cheating because many of the knucklers used their entire hands rather than just their knuckles.

3. The population definitely evolved. At the start, 48% of the population had "a" alleles and 52% had "A" alleles. This was pretty even and the allele frequency was very balanced at the start. However, by the end of the 8th trial, the "a" had a staggering 70% frequency while "A" only had a frequency of 30%. If evolution is a change in allele frequency over time, then a change of this scale is definitely evidence that natural selection took place.

 4. In this lab, there was a lot of other factors that affected results. Some people didn't have pockets which prevented them from gathering much food. Others weren't very fast at running or picking the corks up which prevented them from getting to the food. Many participants also cheated by not using their assigned phenotype, which allowed them to unfairly sway the results in their phenotype's favor.

5. If food was larger, then disruptive selection may take place. This is because the stumpies would be able to pick it up with their palms and the pinchers could grasp around the food with their long fingers. But the knucklers, whose phalanges can't stretch that far apart, would die off. If the corks were smaller, I would expect directional selection in which the knucklers and pinchers are favored due to their better dexterity.

6. Yes. If one allele had complete dominance over the other, then the pinchers might have become extremely rare. This would doom the population to being outcompeted by other species because only the inefficient knucklers would be common.

7. Natural selection is the mechanism, while evolution is the actual change that results from the shift in allele frequency.

8. The pinchers tended to mate with other pinchers because we knew that the "aa" phenotype tended to survive better. Also, the stumpies would try to mate with knucklers or pinchers because that would allow their child to be a knuckler. If mating choice was random, knucklers would easily become the majority phenotype.

9. In evolution, the population evolves. Natural selection acts on phenotypes, but as a result the genotype frequency changes. For example, if black fur helps with camouflage, then natural selection will cause the black fur trait to become common. But various genotypes can cause black fur and natural selection does not discriminate between those.

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