Unit 10 Reflection

Unit 10 was the last unit and was about Human Anatomy and Physiology. We learned about the different systems and how they all work together. The circulatory and respiratory systems work together. The lungs supply oxygen to the blood, and the heart pumps the oxygenated blood to the cells around the body. Then, it is sent to the longs again to receive oxygen again and the cycle continues. 

Flow of blood through the heart 

The nervous system contains the Central nervous system and Peripheral Nervous system. The CNS contains the brain and spinal cord, while the PNS contains the cranial nerves, spinal nerves, sensory neurons, and motor neurons. They pass signals between each other and within their own system so our bodies can function. The endocrine system is made up of glands. The glands produce hormones (chemical substances) that help regulate different things in our body. For example, the parathyroid gland regulates calcium. The digestive system helps with the break down and absoption of nutrients into the body. 

Digestive system

The immune system and the lymphatic system work together to keep pathogens out of the body, and to keep the body healthy and safe. The only lab we did was the fetal pig dissection . It helped us understand where all the different organs were located and how their different functions worked together. 

I wonder how our organs develop and grow. I want to learn more about how the brain works since it is the control center of our body. How did these organs develop over time? How did the human brain develop to become so different? How did humans start learning more about our anatomy? 

Looking back to the start of freshmen year, I think that I have grown a lot. In the Jean Lab conclusion , my post was super statistical and boring. Over time, they became more interesting and descriptive, not just about the data. My blog posts also became longer and more detailed. My first unit reflection was just a giant list of things we learned , but now they are more about explanations and connections. Writing is something I struggle with overall ( I am a slow writer), but I think that I have improved a lot in speed and quality. Besides the blogposts, I have grown as a student since I now take a lot more interest in exploring more based off what we learned in class. 

Pig Dissection

The purpose of this lab was to identify the different systems and to see how they all work together.  It helped us learn more in depth about the different systems, and we could see their relations in a real organism, not just in a diagram. We could see more clearly how they all worked together and their importance to each other. For example, we saw the heart was placed between the lungs and the main arteries and veins, showing the relationship that the circulatory and respiratory systems support each other. The heart needs oxygen from the lungs so it can pump oxygenated blood to the whole body.The anatomy and physiology of the pig is very similar to humans since they both are mammals. My favorite part of the dissection was making the cuts, which were exciting. It slowly revealed all the inside organs, until eventually almost the entire anatomy was revealed. I think that this dissection was a valuable experience because it helped me to pull together all the vodcasts and understand how everything was related. I was not able to understand it through separate diagrams.

endocrine system 

external anatomy 

respiratory 

 

digestive system

urinary and reproductive system 

circulatory system pt 1

circulatory system pt 2

20 Time Final post

Ella's and my 20 time project was to follow the model of the fun theory to try and make everyday activities more fun to improve peoples' health and happiness. Here is a summary of our experience.  For a month we brainstormed different ways to make activities more fun. We only started conducting experiments in early April, since our experiments had a lot of variables, or the ones we thought of were too complex. Our first experiment aimed to make our school cleaner by adding basketball hoops over trashcans  to making throwing trash away more fun. We found that after adding the hoop there was a spike in the amount of trash people threw away. Once we took it away, the number dropped.

Amount of trash people threw away in the team room

We also tried to make homework more fun by giving people small tests with "Fun pens" (sparkly gel pens). The people who used the fun pens said it was more fun than a regular pen and they would take the quiz again. One person who used a regular pen said she would take it again if she had a fun pen. There are still a lot of ways that we can make life more fun, but it is difficult to be creative.

Our TED talk went well overall, although it could have been better. I was not happy with my stage presence and projection, since I know that I can utilize the stage better. We memorized certain parts and were able to replicate it. However, I forgot to  state our original thesis that tied in all the concepts, but Ella said it later. I think we meet all the parts of the rubric, except we went really fast. When we timed ourselves, we were at 5 minutes 30 seconds each time, but our actual talk was 4 minutes 18 seconds. The balloon idea actually worked surprisingly. I was worried that it would take away from our talk, but it seemed to enforce it. Ella and I met up twice outside of school for 6 hours total to work on the talk. We skyped several times and practiced it completely at least three times. I learnt that a lot of work goes into things that last for less than 5 minutes. Listening to other talks was really interesting because I did not know what to expect going in, and I learnt what everyone was interested in

20 Time Individual reflection

For my twenty time project, I wanted a project that had something based in psychology because it is super fascinating to me and I never really get a chance to explore it. Both Ella and I wanted a psychology based project.  After doing some research, Ella and I came across the "Fun Theory". It seemed interesting and, at the time, the most reasonable theory to use in our project with the materials we had. It showed cause and effect between making boring things fun and a willingness to do it more. We chose to try and answer the question how can we use the Fun Theory to improve our everyday lives? Our goal was not to prove the fun theory, but rther to find a way to use it. This really challenged my creativity, as we needed to think of mundane/hated activities and how to make them fun. I wanted to find a way(s) to slightly improve my daily life, and if possible, the life of the student body at Saratoga High. 

First, we had to come up with a list of things we disliked, found boring, or were generally mundane. This was quite easy. It was more difficult to figure out ways to make them fun that were doable,cheap, and not time consuming. For example, we thought about making fancy shapes out of disliked food such as tomatoes. We realized that people may eat them if someone else made it for them, but were not going to take the time to do it themselves. If we found a way to make something fun, we quickly asked around and found that most people did not consider either the activity boring or the improvement fun. We kept on getting stuck on the definition of the word "fun" and often switched around our main question. This was quite time-wasting. Three vague experiment ideas only came up by the beginning and middle of April. 

The project was not very successful. It is definitely something that needed to be long term. Our brainstorming took too long and gave us too little time to carry out the experiments. We needed to spend a lot more time on this outside of allotted twenty time. We have gathered data from one experiment, and are trying to finish up two short ones. Realistically, only one will be completed. I learnt that it is good to have a solid plan before starting, and too not get very caught up with brainstorming. It is easier to have a fixed product or conclusion to reach than to build off a theory. If I could do this project again, I would definitely do something psychology based again, but with more reliable results/experiments/products. I would have tried to answer a question rather than apply a psychological theory to everyday life. For the Fun theory, I may have tried to prove it or see if people use it in their daily lives. This project feels that it is just starting. Potentially, it could be investigated very thoroughly, however, we would need more resources. It was difficult to find a list of ways to improve daily life without set-up, expenses or on a daily basis. We would have liked to have a longer list to share with our classmates on how they can improve their daily lives. Unfortunately, we only have a couple. I may try to find fun improvements to my daily life or give suggestions to my friends if they complain about a boring aspect of their lives.

Unit 9 Reflection

In this unit, we learnt about the kingdoms and phyla of the taxonomic levels, including some major classes. The tree of life was a huge concept in this unit. It shows how different kingdoms have evolved over time, how some emerged, and from where they got their features. These features develop through natural selection. All living organisms are divided into different levels: domain, kingdom, phylum, class, order, family, genus and species. The division helps scientists study organisms that are more closely related and learn about specific characteristics. To see the evolutionary relationships, scientists use cladograms, which show where new traits appeared

Photo link

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There are three main domains and six kingdoms. Domain Archaea contains organims that live in extreme environments. We do not have much information on them since they live in places that are difficult to reach/study. Domain bacteria contains eubacteria. They come in a variety of shapes and produce antibiotics. Viruses are classified as non living,but they contain genetic material. Once they latch onto a host, they come to "life" and begin making copies of themselves to infect other organisms. Some people theorize that viruses were the basis of life, and that it evolved to become alive. Domain Archaea and Bacteria were the earliest forms of life and they may have reconnected to form Domain Eukarya, which contains the forms of life that we are more familiar with.

Kingdom Plantae is made of plants. All of them perform photosynthesis to obtain sugars. All phyla except bryophyta use a vascular system to transport nutrients. Phylum Angiosperm are all the flowering/ fruit plants which provide us with fruit to eat.Kingdom Fungi is quite different from plants. Their cells walls are made of chitin and they absorb food through their hyphae. They can reproduce sexually or asexually. Along with bacteria, they are the main decomposers in any ecosystem.

Most animals - 97% - do not have backbones. These are called invertebrates.Sponges are the most primitive types of animals, since they are closely related to protists. Cnidarians are similar, but they have specialized tissues. Flatworms are solid and can move around, but their guts are incomplete or not there. Mollusks have a complete digestive tract and a type of respiratory system. The evolution of traits to support more complex life keep developing. Phylum Arthropoda are even more so adapted. They have exoskeletons and sensory systems/ antennas. Insects are the dominant arthropods, and to the disgust of some humans, can be found almost everywhere. Crustaceans are the marine version of arthropods. Phylum Echinodermata is the closest related to vertebrates, they are on the same branch. They use a water vascular system.

Vertebrates make up the other 3% of animals. All belong to Phylum Chordata. Class Agnatha were the first recognizable vertebrates but were jawless fish. Condricthyes are fish that have cartilaginous skeletons and jaws. Osteicythes  have jaws and bony skeletons. They have an operculum that helps protect the gills and move water over them so the fish does not have to constantly move to live. The fish develop over time due to natural selection. Amphibians are the transitionary class since they can live on both water and land. The tiktaalik was the transitionary animal. Its fins became strong enough to support its weight so it could walk.

Tiktaalik

Reptiles are cold blooded and have a three chamber heart like the amphibians. Classes Aves and mammalia are warm blooded and have four chamber hearts. Class Aves consists of all the birds. The archaeopteryx was a animal that was between the stage of dinosaurs(reptile) to birds. Mammals are the organisms we think of as "animals". They have active large brains, complex social, feeding and reproductive behaviors and hair. We are mammals. Millions of years of evolution has helped shaped our species today.


The concepts were not hard this unit, however, it was a lot of information to absorb. I kept mixing up different characteristics of different phyla.I want to learn more about the transitionary animals. How do the animals change anatomically? Will the human race evolve into a new species? Why have we not discovered all the species on earth yet? How come the human race is dominant and if we go extinct who will take over next? Are humans doing a bad thing by keeping endangered species? Why do people misclassify organisms all the time?

For my What on Earth Evolved? presentation, I chose the Archaeopteryx. It fascinated me because it was an extinct species and I wanted to learn more about it. I learnt some very interesting facts, since the species has a lot of mystery and controversy surrounding it and the facts changed almost every year. My presentation could have gone much better.  I was super nervous because it was my first presentation in biology so I did not know what to expect. I did not have many words but rather more pictures. I like to explain and not be held down to a script. I could have explained things a lot better and I should have run through it out loud a few more times. I felt that I held most people's attention since there was not much for them to see on the screen. For my TED talk, I will definitely practice more and stay calm. Although it is May, I am proud that I stuck to my New Year's goal all through April, especially with biology. I finished vodcasts the day they were assigned and I started on my presentation three weeks before. I also spread out my studying the best for this test.

My Inner Fish

   Your Inner Fish by Neil Shubin explains how our ancestors that may look very different from us gave us many of our characteristics today. Fish are the most distant ancestors of our modern hands. They were the first to show the system of one bone, two bones, many bones in limbs/fins. Scientists studied fish embryos and found many fossils to support this. Many organisms look the same during early stages in development until Hox genes turn on and specialize the cells to grow into whatever the organism is.
   The sonic hedgehog gene emits a signal to tell cells where they are in the body. Based on that, they grow certain limbs and fingers. The closer the signal, the pinky finger grows and the furthest the thumb. This is related to the specialization of cells. The sonic hedgehog gene may have developed through natural selection as organisms started becoming more complex. I wonder how the sonic hedgehog gene works in detail and how it came about. Would having extra finger through mutation actually become favored?
   The tiktaalik is one of the greatest finds connecting fish to land animals. It swam mostly, but its fins could support its body weight enough so it could walk on land. This trait came through natural selection - favoring stronger fins and wrists. Tiktaalik could also move its neck to watch for predators. It was the transitionary fossil between fish and amphibians. The first fossil was almost a rare specimen, which is a very lucky find. I wonder how one scientist was so lucky that he discovered so many breakthroughs in science? How did it stay intact for millions of years? How did the scientists know where to look? If it had a favored trait then why did it die out?
   The video also talks about mammals and reptiles- how they passed down their sense of hearing. There was one jawbone and one ear bone. Over time, the ear bone and parts jawbone formed the ear. Mammals also developed their hair because of the cold and a way to communicate with other animals. The parts of our body we use everyday and almost every second come from our ancestors that look nothing like us.

Fish fin developed into hand

Photo link

Giant Squid

The Giant squid is one of the largest invertebrate and animal species. The only larger species of squid is the colossal squid. Most scientists believe that there is only one species of giant squid although some researchers believe there are almost 8 species. There is no agreement since it is so hard to track because it lives deep in the ocean and there are very few specimen already. It belongs to the genus Architeuthis in the family Architeuthidae of the order Teuthida to the class Cephalopoda. It is under the phylum Mollusca. Animals in this phylum need at least one of the following: a radula, mantle, or ctenidia. A giant squid has a mantle, eight arms and two longer tentacles (longest known tentacles of any cephalopod). The arms and tentacles make up of the squid's great length, making it much lighter than its chief predator, the sperm whale. Giant squids' mantles are not known to exceed 2.25 m (7.4 ft) and the length of the squid excluding its tentacles rarely exceeds 5 m (16 ft) , so  their size is often exaggerated. Since we cannot track them well we know very little about their reproduction cycle, but they definitely reproduce sexually. Little genetic variations through giant squid individuals suggests that there is only one species of giant squid. I wonder if there is a better way for us to learn more about them. Why is there only one species?

Works cited: 
https://en.wikipedia.org/wiki/Giant_squid
http://ocean.si.edu/giant-squid
Picture

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.

Link 

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.
The earth's history is longer than anyone can comprehend. Species have been evolving on this planet for billions of years. The timeline has been divided up based on major extinctions and emergence of species.

Link

This unit was relatively easy for me. The only difficult thing is wrapping my head around the scale of the timeline. Also I am not sure exactly how unicellular organisms became multicellular organisms and how those grew into plants, animals etc.
I still have many unanswered questions. Is it possible that if even one event from the past had not occurred then we would not be here? How did species evolve if they were mainly asexually reproducing (bacteria, unicellular)? If there have been several mass extinctions, then is it wrong that we are stopping some species form going extinct? How does "natural selection" choose the better genotypes if each organisms' genotype is randomly assigned?
Going back to the New Years Goals, I have been keeping up quite well. I started studying 3-4 days in advance and I utilize my free time to finish homework if I know I will not get time.

To be more assertive I have tried to be more honest, but kind, to people. I am not aggressive, but sometimes passive aggressive and I try to stop myself whenever I feel that I am being more aggressive. I need to stop being passive in situations where I stay passive to avoid trouble to difficulty in solving the problem.

Geologic Timeline Individual Reflection

The first major event was when cyanobacteria began photosynthesis during the Proterozoic Epoch. Once cyanobacteria began photosynthesis, they put a lot of oxygen into the atmosphere, helping oxygen persist in the atmosphere because it was usually consumed as soon as it was put out. More oxygen lead to a decrease in some bacteria but multicellular algae, and toward the end of the Proterozoic, the first animals started coming up. This was the most critical event in developing life since without large amounts oxygen in the atmosphere, humans would not survive.

The second main event was the extinction at the end of the Paleozoic Era. The mass extinction got rid of 80% of all the species on earth. It affected marine communities the most by far, causing the extinction of most of the marine invertebrates of the time. Some groups survived the Permian mass extinction in greatly diminished numbers, but they never again reached the ecological dominance they once had, allowing another group to dominate the sea. However, this massive loss of life lead to an explosion of life. The new period that began was the time of the dinosaurs. Life was never the same. 

The third main event occurred in the tertiary period. Birds and mammals were began to radiate and flowering plants and insects began to dominate. We know this because the fossils of this time period indicate that. The domination of mammals was the beginning of the evolution of homo sapiens. If mammals began to dominate and grow later or not at all, then humans would probably not be at the stage we are now, or we may not have evolved to be the way we are right now.

The first billion years or so consists of no life on earth.  Life shows up quite late on the timeline. The dinosuars existed on the earth for approx 1/3 of all of its history and were the humans of the Mesozoic Era. The only thing that we have evidence of their existence is fossils. Humans show up only in the last 12,000 years. Im amazed that the earth went so long without life and yet we have changed the earth more than it has probably changed in the past 4.6 billion years. 

We have had a gigantic impact on the earth compared to the amount of time the human race as we know it has existed. All of recorded history does not even make up one second in the clock of the universe. We are already cutting down all the forests, polluting the rivers, and killing off species on a planet that has been around nearly 500 times longer than we have of recorded history. A planet that has taken 4.6 billion years to be made is being destroyed in a few centuries. I think it is far too late to turn back now because these precious things cannot be replaced for a few centuries, and that is long enough for the human race to go extinct. 

I wonder why only our planet evolved the way it did. How do we know that there were not human-like creatures before us? How much longer can the earth sustain us? What event will mark the beginning of a new era or epoch?

Hunger Games Lab

1. In this lab, we went outside to the field, and each of us was assigned a way to pick up "food". There were three different ways to pick up food: using both your wrists, your thumb and index finger, and in between your middle knuckles. This simulated natural selection and competition. When the people that had enough food survived and the others "died", coin flips simulated sex and meiosis. When the coins were in the air, that simulated crossing over and when they were put down together that simulated sex.

2. The pinchers were the best at picking up food. They had a good grip on the food and could stretch their beaks/fingers the furthest apart so they could technically pick up 4 pieces at one time.

3. In this lab we asked the question: Do populations evolve? We found if the gene pool and allele frequency has changed over time, then evolution has occurred. At the beginning of the lab the "A" allele had a frequency of 52% and the "a" allele had a frequency of 48%. They had an almost equal ratio. In the middle of the lab (trial 5) the "A" allele had a frequency of 34% and the "a" allele had a frequency of 66%. At the end of the lab, the "A" allele had a frequency of 28% and the "a" allele had a frequency of 72%. We can see that the "A" allele frequency steadily decreased over time while the "a" allele slowly decreased over time. This means that the population evolved since the allele frequency changed over time.

4. There were many random and non-random things in this lab. Mr. Orre randomly placed the food on the ground and it was random for who was standing closest to the most amount of food. The competitiveness and fitness of the students was also random because that played a role in determining who got the most food.  The places where people stored their food was also random, because some people had big pockets, some had small pockets, and some used their jackets. The flipping of coins and offspring were random. The mate choice was not random. The way people picked up their food was not random since they were assigned a certain way to do it. This affected how well certain species survived or died off. This  could have caused certain alleles to be more dominant because even though the method of picking up food may have been easy, the person may be very slow or have no place to store their food once he/she picked it up.

5. Yes, the results would have been different if the food sizes were larger or smaller. The stumpys would have died off much more slowly if the food sizes were bigger, because then it is easier to pick up. The knucklers would have had a little harder time picking up food. because they cant stretch their fingers further apart then they did with the corks. The pinchers would be better off because they would get a better grip on food. If the size was smaller, then stumpys and knucklers would have died off more rapidly, but pinchers would have grown faster. In nature due to a genetic drift, the size and type of food avaliable may be different. For example, Darwin's finches had smaller beaks because the seeds they ate were small and soft. Later, a drought occurred, and the main type of seed available  was hard and big, so the finches slowly decreased in population size or evolved.

6. Yes there would be a huge difference if there was no incomplete dominance. Every time  knucklers mated they would produce a stumpy. The pinchers would start inbreeding a lot more to preserve their trait. The stumpys would overtake the population but that is not necessarily the best trait because it makes obtaining food difficult.

7. Natural selection causes evolution to occur. Natural selection acts on the phenotypes that seem best suited for the environment by ensuring that only the better traits can mostly survive and reproduce. This changes the allele frequency therefore evolving the population in their genotypes which produce certain suitable phenotypes.

8. Most people did not have a main strategy while obtaining food. It felt a lot similar to "each one for himself". Individuals with the same traits did not try and get together. Some people cheated and grabbed handfuls of food, which could have resulted in errors in the results. People did not mate with who would help them survive better, but rather who would help them reproduce better offspring. The knucklers seemed to mate with the knucklers to give their children a better chance of being a knuckler or pincher rather than a stumpy. Pinchers bred with pinchers because they did not want their children to be a knuckler. It was difficult to tell the mating preferences of the stumpys because they often died before reproducing, but they tried to mate with pinchers to have a knuckler rather than a stumpy. This caused there to be a lot of knucklers in the population quite consistently. These mating choices also played a role in the decreasing number of stumpys. In nature, peacocks have large beautiful feathers to attract mates because strong feathers indicate they are better at obtaining food and the colors are attractive.

9. In evolution, the population as a whole evolves. Individuals cannot evolve since they are stuck with what their parents gave them. Natural selection acts on both the phenotype and genotype. It wants the phenotypes that reproduce and survive better, so to obtain these traits it acts on the genotypes, especially if it is a mutation, that caused the favorable phenotype. It can also act directly on the genotype to get rid of certain genetic diseases.

10. I still have a lot of questions. Could we have evolved into something completely different if a certain event had not happened? What will we evolve into? How exactly do we track evolution and know for sure what changes happened in allele frequency? Why did people reject the theory of evolution? If they rejected it, what did they believe in?

Graph showing change in allele frequency over time 

Everyone runs towards the food (Picture credits to Kimi) 

Bird Beak Lab

Part 1
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?" We found that if there are individuals with better traits leave more offspring, then the tweezer beaks will survive and pass on their genes. The tweezer beak produced 18 offspring, which was the most amount of offspring produced by a certain bird in the group. The tweezer's beak was far more accurate to pick up food and it was the easiest to use to pick up food. This lead to the tweezer getting a lot of food/energy so it could produce lots of offspring.

We also found that if the population looks like the winners, then the tweezer beaks will become dominant in the population. The tweezer beak's offspring made up 37% of all of the offspring in the group. The spoon made up 8%, the binder clip chicks made up 20% and the scissor chicks made up 35%. The tweezer chicks are slowly making up a bigger percentage of all of the offspring, because they are the "winners" since they are reproducing the most.

Part 2
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?" The tweezer beak collected 7 seed pot plants or approximately 2 chicks in part 1. If the seed pot plants died out, then we will see a slight decrease in the tweezer beak chicks. Our hypothesis was not supported, and in fact there was an increase in tweezer chicks. The tweezer beaks produced 23 chicks in part 2. This is five more offspring than it produced in part 1. This meant that the shortage of food did not negatively affect the tweezer beaks.

Our data was unexpected because shortage in food usually leads to a decrease in energy and offspring, but the tweezer beaks saw an increase in offspring.There could have been some errors. First, this lab required a little bit of practice for the humans who were simulating the beaks, and so they could have gotten much better with using their beaks as the lab progressed. This could have lead to the increase of tweezer chicks in part 2 instead of a decrease, because I became more skilled with picking up other types of food. Second, sometimes everyone "ate" food for different times because we were not aware when the music started and stopped exactly. This would change the amount of offspring by at least 1. Due to these errors, in future experiments I would recommend having everyone rotate which "beak" they used and counting before starting/ stopping the music.

This lab was done to demonstrate Charles Darwin's main observations and conclusions. From this lab, I learned how evolution occurs which helped me understand how there are winners and losers in the population. I also better understand how the gene pool changes. Based on my experience in this lab, I better understand how Darwin's conclusions are the results of evolution.

Unit 7 Reflection

This unit was about ecology and the harmful effects humans can have on the environment. Ecology is the study of interactions between different organisms and the environment. The first thing we learnt about was the different trophic levels and their interactions. The main source of energy, as we learnt in Unit 3, are plants. Plants are autotrophs/producers and they create their own energy. They are then consumed by heterotrophs. Food webs and food chains are used to show the main transfers of energy.

https://en.wikipedia.org/wiki/Food_chain

 Only 10% of energy is transferred from one level to the next, and this is shown in energy pyramids. This is mostly interactions within populations. Populations can be controlled by several different factors. Emigration/ Immigration and deaths/births are the main factors that control population growth, but limitations of resources is also a major factor. Right now, humans are exponentially growing, but we will soon reach our carrying capacity. Our Earth has limited resources and they are all recycled in Nutrient cycles. Ex: in the water cycle, water evaporates into the sky and clouds can be carried to other places where it rains, and that area receives water. Nitrogen in particular is crucial to life on earth because it forms DNA and RNA.
Click here for a longer explanation on the importance of DNA and RNA: http://revavaidyabiology.blogspot.com/2015/12/unit-5-reflection.html
However, our earth is not as healthy as we would like it to be. We are in the middle of a sixth mass extinction and climate change is completely misaligning entire ecosystems. One thing we can all do is to think globally, and act locally. The first step to change is awareness, and many individuals all add up to a big change.
This unit was quite easy, but we went so indepth on each area that I felt like I forgot a little bit of the previous vodcasts.
I still have quite a few unanswered questions. Is it too late to change the earth? How will species adapt in response to all of these threats? Can one person REALLY make a difference? How do we know anything about species that went extinct before technological advances?

The Biologist conservation project was a mix. We all worked well as a team, which is not surprising because on the preferred method of conflict management assessment we all scored high on "assertive". However, we rushed filming a bit too much because we were all so caught up in research. Researching was interesting, and we learnt things that we would not have otherwise. The desert is much more complex and in much more trouble then we originally thought. This felt very slow because last unit was all about labs and being active. 

Click here to watch our conservation biologist project: https://www.youtube.com/watch?v=rv7fgVoFFNg

Reflecting back on the new years goals in the last unit reflection (click here http://revavaidyabiology.blogspot.com/2016/01/new-years-goals.html) , I am keeping up better with my goals. I am maintaining the grades I am satisfied with, and I am using my time more efficently. The only goal I'm am falling short of is effective studying. 

Unit 6 Reflection

This unit was about biotechnology. We learnt about how there are many ethical questions currently surrounding the biotechnology industry, because scientists and others are concerned about the ethics and values of each person about genetic engineering. Then, we learnt how scientist recombine DNA in bacteria. They take the plasmid and insert the gene into it. Then, they place the bacteria in broth to make them grow and place them in the antibiotic that the bacteria should have resistance to. All the bacteria without this gene/plasmid will die. To learn more about this concept, we did the recombinant DNA. We simulated restriction enzymes cutting out genes and placing them into plasmids with the Recombinant DNA lab.
To read more about it  click here:  http://revavaidyabiology.blogspot.com/2016/01/recombinant-dna-lab.html
Then, we learnt about the basic process of replication of DNA and analyzation. In order to reenforce the concepts we did the pGLO lab. We inserted plasmids into DNA by mixing certain bacteria with a solution with the GFP gene and moving it from cold to hot temperatures so it would absorb it. Only those with the GFP gene would glow.

Click here to read more:  http://revavaidyabiology.blogspot.com/2016/01/pglo-lab.html . However, before this we did the gel electrophoresis lab in class to get first hand experience on analyzing DNA. Click here: http://revavaidyabiology.blogspot.com/2016/01/candy-electrophoresis-lab.html. We learned how to use a micropipette to insert the DNA samples and references into the gel wells. In this lab, we did not use DNA, but instead used commonly color dyes from candies.

I feel that I understood this unit quite well, especially because of the labs. One thing that was difficult however, were the labs, because we had to be much more precise and careful, otherwise we would not get the desired results. This unit expanded on Unit 5 which was about DNA. I want to learn more about how do we use other forms of life other than bacteria in biotech. When will we be able to alter human DNA? Will it ever be widely used? Could this play a hand in evolution?

So far in relation to my New year's goals, I have not been very successful. I planned on studying a week and a half before tests, but am only studying 3 days before, or just on the weekend and then the night before.  I started making flashcards for all tests so I will have them to study for finals. I have also not been able to finish all my homework the day it is given: however, I have been more productive during tutorials.

pGLO lab

1.

Plate	Number of Colonies	Color of colonies under room light	Color of colonies under UV  light
-pGLO LB	carpet	brownish yellow	whitish blue
-pGLO LB/amp	0	N/A	N/A
+pGLO LB/amp	150-200	brownish yellow	whitish blue
+pGLO LB/amp/ara	47	brownish yellow	glowing green

2. The bacteria gained two new traits. The bacteria in the "+pGLO/LB/amp/arab" glowed under UV light and gained resistance to ampicillin because they were able to survive in the ampicillin and grow into 47 colonies.

3. On the "+pGLO/LB/amp/arab" plate, there were around 47 colonies. There was a lot of empty space, almost 1/2 of the plate was empty. Each bacteria that transformed would have multiplied into a colony, therefore around 100 bacteria were in the 100 micro-liters, and half of them died. On the "+pGLO LB/amp" around 150 colonies were on the plate. However, since we spread the bacteria all around the plate and there are empty spaces, we must have put around 250 bacteria. On the "-pGLO/LB" there were many more bacteria than on the other plates that made it onto the plate because almost the entire plate was covered. On the "-pGLO/ LB/ amp", we do not know how many bacteria made it onto the plate because they all died on contact since they did not have the ampicillin resistance.

4. The glowing is caused by GFP or Green Fluorescent Protein.  The GFP is "turned on" in the presence of arabinose, and starts expressing its traits. So arabinose causes the cells to glow green. 

5. There are many uses of GFP for scientists. In cellular biology, GFP has been used as reporter gene, cell marker, fusion tag. This means that if the cell glows then the scientists know that whatever gene they inserted into the cell is also being expressed, because GFP is attached to that protein. In the early 1990s, molecular biologist Douglas Prasher, used GFP to design probes, a technology involving fragments of DNA to detect the presence of nucleotide sequences. GFP is also used to to make the resultant protein react to wider wavelengths and emanate different colors. 

6. Genetic engineering can be used to alter crops so that they become more resistant to pesticides and pests.  It can also be used to make bacteria mass produce insulin for diabetics. 

under normal light

All under UV light

UV light from the top

UV light from the side

Source: 

https://embryo.asu.edu/pages/green-fluorescent-protein

Candy Electrophoresis Lab

1. Our blue reference was slightly ahead of our blue sample. We had no orange dye in our samples unlike our reference. The green sample separated out into blue and yellow, which we expected because green is made of blue and yellow. The references were a bit brighter than the samples. All of them moved in the right direction.

2. Citrus Red 2 would move at the same speed as Red 40, Yellow 6 and Yellow 5  because they are all made up of three sugars. Fast green FCF and Blue 1 would move at similar speeds because they are both made up of 5 sugars and have a similar structure.

3. Dog food manufacturers put artificial food colors in dog food to modify the appearance of the dog food. They try and use the food colors to make the food look richer and, therefore, healthier. People are tricked into buying these foods because they think it is the best thing for their dog.

4. Artificial food colors may be preferable to natural food colors because, while they are unhealthy, using a smaller amount probably results in a darker and richer color. This appeals to customers and the manufacturers save money.

5. Length affects how far the colored solutions migrate because the shorter it is the easier it is to migrate faster. Structure would also affect the speed. If the structure is thin and long, then it will be much slower than a short and contained one.

6. An electric current moves the dyes through the gel. The dyes have a negative charge, and  a positive charge is put at the other end of the box and a negative charge is behind it. The dyes repel the negative charge and are attracted to the positive charge which causes them to move.

7. The gel is filled with tiny holes. The smaller the molecules are, the easier it is for them to avoid the holes and get to the other end. The bigger molecules take a more time to navigate around the holes, causing them to get left behind.

8. The DNA with the weight of 600 daltons would be the farthest from the well. Then it would be 1000, 2000, and 5000 respectively. The heavier pieces of DNA would be bigger and the lighter pieces would be heavier. The smaller pieces of DNA always travel faster than the bigger ones. (refer to question 7) 

Before the current flows

In the box

Out of the box

The color dye samples

Recombinant DNA lab

First locate the gene of interest and organism to insert the gene into, which was the insulin gene in this lab. Then, obtain a plasmid from bacteria and what is its antibiotic resistance. In this lab, our plasmid was resistant to ampicillin.
Next, find a restriction enzyme that makes one cut in the plasmid and one above and below the gene of interest so it can be taken out and inserted into the plasmid. Restriction enzymes cut DNA wherever they find a specific sequence. It cuts using "sticky ends" so that the DNA base pairs can easily bond together. We used Hin dIII because it made only one cut in the plasmid and the closest cuts above and below the insulin gene. If the enzyme had made two cuts in the plasmid, then the DNA would break apart, resembling two unattached semicircles.
Then, add ligase to stick the ends of the gene into the plasmid. After that, plate bacteria on petri dish with the antibiotic mixed. We could use ampicillin since the plasmid we chose to insert the insulin gene into was resistant to it, and only those with ampicillin resistance would survive; therefore, those would be the ones with the insulin gene. We would not use tetracycline or kanamycin because our genetically modified bacteria would be killed because they are not resistant to these antibiotics. Finally, we would transfer the bacteria to a "broth" so they will multiply quickly and then extract and purify the protein the inserted gene produced.
This process is important in our everyday lives because it provides people who cannot produce a certain protein with a way to get it into their bodies, for example diabetic patients cannot produce enough insulin, but because of recombinant DNA they can take insulin injections or pills. This process could also be used to make vaccines and make crops resistant to pesticides or enhance their flavor and nutritional content.

New Year's Goals

Last year/ semester was good, but this year/ semester should be even better!

My first goal is to receive a high A or an A+. The plan I have is as follows: consistently receive good grades on the tests and labs. To do this, I will start studying for my tests a week and a half in advance. I will read the relate and reviews, and then study in depth for 20-30 minutes each night leading up to the test.
My second goal is to manage my time much more efficiently. I will do this by completing my homework on the day it is given, and start planning for long term projects. I will also allot time to study for tests and use tutorials wisely.