Friday, May 26, 2017

Genius Hour Week 3

This week marked the beginning of data collection. After solidifying a plan I started the week by gathering materials. India just happened to have the right material to act as a color filter over the light bulbs, thin plastic folder dividers in green, blue, and orange. I decided where to put the lamps in the room so the lights of one would not interfere with the results of the other plants. I then replaced all the heat lamp bulbs with regular bulbs and tested each one to make sure they functioned. After that I stopped by Paris Farmers Union after school and purchased the subject plants (which turned out to be young onions and not chives). I taped up the plastic dividers so they dangled about an inch from the lamp and placed each pair of onion plants approximately 9 inches from the lamp. I took pictures from side angles and a birds eye view of the positioning of each plant before turning on the lamps. On Friday morning they had been running for 24 hours and I took pictures again to document progress. Now they will be left until school on Tuesday.

Sunday, May 21, 2017

Genius Hour Week 2

This week on Genius hour, Gridley heads back to the drawing board. After some deliberation, I realized there was a very real possibility that the different variables I would be testing to observe physical changes in the Tobacco plants, would simply result in killing them or have no measurable response. Rather than risk explaining a lot of inconclusive data, another idea for a project struck me. Knowing that plants are phototropic and will track movement of light, I want to find out if plants will track different wavelengths to varying degrees. I plan to use chives as my experimental plant as they will be very distinct pointers and will be easy to collect observable data from. I know from class that green is the least useful part of the light spectrum and that plants instead prefer to absorb blues or reds. so I expect that the chives exposed to green light will display the least amount of bending towards the light, in comparison to the other wavelengths. Even if there is no measurable difference between the severity in the chive's tracking of the separate lights, that alone would tell me that plants still track all colors equally when it is the only light source available. Hence no matter the outcome, a solid conclusion can be drawn.

Monday, May 15, 2017

Weekly Bio Blog (Heart Week)

This week was all about heats, however it was shortened for me because I left Thursday for my class trip to France. We started the week off by watching an episode of documentary series called Blood and Guts, on the history of open heart surgery. The show made me realize how recently open heart surgery emerged in history, and that until WWII it had never been accomplished in the field. Even when surgeons felt comfortable that open heart surgery wasn't a taboo crap shoot anymore, doctors still had to be limited to 4 minutes of operation time before the patient died from oxygen deprivation, a side affect of being put under. And only decades ago they realized that they could extend the time by exposing their patients to cold temperatures thereby lowering the rate of oxygen consumption by the brain.
That night we over viewed a short packet detailing the anatomy and functions of the heart in preparation for Tuesday. Mrs. Cole's husband supplied the classroom with enough deer hearts from his hunting excursions that every pair had their own heart. Tuesday was only an exploratory day and no incisions were made. Instead we just got familiar with the external. Wednesday we began actually dissecting the heart and explored the Atriums, Ventricles, Aorta, and Vena Cava. Deer hearts are relatively close in size and structure to human hearts making it a very good experience in understanding the physiology of our own hearts beating in our chests.

Sunday, May 14, 2017

Genius Hour Week 1

This week in Genius hour was all about brainstorming. I struggled to come up with an idea all the way until Friday. Given complete free range and no restrictions is always tricky for me because I never know where to start. There were plenty of topics that would interest me to research but the tricky part was choosing something that given the confines of budget and access, would be able to show case through a tangible experiment. This year I've been intrigued by what can be inherited and passed down that aren't clearly labeled in DNA such as instinctual behaviors and the like. A snake at birth simply "knows" how to strike and coil and a caterpillar just knows how to craft a chrysalis without ever being taught. I will be growing tobacco plants in separate environments to show that organisms with the same basic DNA can have their physical attributes altered by external forces, possibly suggesting that DNA isn't the end all be all.

Saturday, April 29, 2017

Weekly Bio Journal #8 April 29

This week revolved around our transpiration lab. Transpiration is the process by which moisture is carried through plants from roots to small pores on the underside of leaves, where it changes to vapor and is released to the atmosphere. Our task was for each group to test a different variable and observe how it may affect a plants rate of transpiration. My group tested how changes in pressure can alter the transpiration rate. Our actual results were difficult to interpret because the initial set up of the pressure vacuum was difficult to create and may have been done incorrectly. We placed the plant stem and leaves upside down in flasks and stoppered the end with a tube connected to a pipette that would measure the rate of transpiration. What ended up happening because the experimental plant was in a closed environment (in order to create a pressure vacuum), the water levels would drop only to rise again later as all the water cycled through had no where to evaporate to except back into the water well. We shall see how we interpret our findings next week. We also completed a packet on the structure of neurons and took notes on Paul Anderson's Podcast on animal communities, and animal ecosystems.

Friday, April 7, 2017

Weekly Bio Journal #7 April 7

This week in biology we started off by taking a quiz on inheritance. This took most of class so we spent the remainder discoing 4.11 and 4.12. That night we watched a 15 minute video on the evolution of stickleback fish and how after generations of living in freshwater, something in their genetics stopped coding for a pelvic spine. From observing these fish scientists learned that our DNA can still possess a gene but choose not to express it through a process called gene regulation. These regulatory switches known as "enhancers" in eukaryotes are specific areas in the DNA where specific activator proteins will bind to turn the gene on or off. What is interesting is the same gene can be expressed in one location on the organism while not expressed in another. While it is the same gene throughout the body, there are multiple switches that can enable or disable it in the selected region.
We studied the first section of the regulation unit this week as well and learned about developmental genetics. The key information here was how every cell in our body can contain the same DNA yet have vastly different functions, Enter the process of differentiation where at the cells early stages it recieves signals from surrounding cells that determine its developmental pathway. We also learned about transposable elements which are non-coding DNA segments that catalyze their own replication and movement throughout the genome. Wednesday the Juniors were out taking the SAT and we spent the next two days working on a specific presentation of a regulation system (circulatory, exretory. nutritional, ect.). This is to famiiorize ourselves with the systems we will study this unit of regulation

Saturday, April 1, 2017

Weekly Bio Journal #6 April 1

This week in bio we focused on modes of inheritance. The biggest part of the week was our virtual fruit fly lab. Here we were tasked with crossing specific traits from fruit flies and from the resulting phenotypes of offspring from first and second generations, we were to predict the genotype of the parents and the inheritance pattern of the traits. We would test our hypothesized inheritance pattern by entering the expected values as predicted by the ratios given by the inheritance pattern, into a chi-square analysis. The first two crosses of fruit flies went swimmingly and I was easily able to predict the inheritance pattern. But the third and fourth crosses gave me particular trouble. The root of the problem for cross three was because when I got home I accidentally gave the wrong gender the trait of white eyes. This trait was supposed to be sex linked and giving it to the wrong sex altered the outcomes from what was originally intended. The fourth cross was one of our own design and after dealing trying fruitlessly to solve what I had done wrong in the third cross, my patience was thin come the dihybrid of the fourth cross and I was unable to accurately predict the inheritance pattern. When I am given known genotypes it is easy for me to predict the probability of certain outcomes, but it is harder for me to work backwards and determine inheritance patterns because there ares so many patterns from, autosomal dominant, recessive, sex linked, co-dominance, incomplete dominance, or perhaps the homozygous dominant or other genotype is fatal. I will need more practice to get it all down,
This week we also completed the Vodcasts on Mendelian extensions in which we learned some of the other modes of inheritance that go beyond the simple Dominant/recessive relationship. We also learned of some specific human conditions and how they are inherited like hemophilia and cystic fibrosis. Thursday we worked on more Mendelian genetics problems and practiced some grid in questions that would appear on the AP exam. Friday we worked on multiple choice questions from an actual AP Exam of a couple years ago in spirit of the up coming exam now only 37 days hence.

Saturday, March 25, 2017

Weekly Bio Journal #5 Mar. 25

The class kicked off this week by completing our second activity on examining cancer patient data. Every one was given a card and on it detailed the gene mutations, on which chromosomes, cell function or cell fate, oncogene or tumor suppressor, and what the resulting cancer was. These cards detailed information from actual cancer patients and together the class compared their cards in order to identify any patterns or trends. What I found from this activity was that many different gene mutations can lead to the same type of cancer and that it often takes more than one gene mutation to cause the cancer. Another interesting fact I learned is that out of the 140 genes found to be linked to cancer, only 9 of those are associated with cell maintenance.
Next we jumped into Mendelian genetics and reviewed how to conduct mono hybrid and dihybrid Punnett squares, and even multiple monohybrid Punnett squares to determine the phenotype and genotype of offspring. These methods came easy to me with a little guidance in the beginning to make sure I was on the right path, and I dare say they are even a little fun. We furthered the Mendelian genetics by practice with pedigrees to determine the genotypes of family trees. Finally we analyzed the data by using chi-square analysis to determine if the observed genotypes were beyond reasonable similarity to the expected outcomes that were given by our Punnett squares. Because I am also taking AP Statistics the conclusions drawn from the chi-square make perfect sense to me and I enjoy chi-square as a tool of analysis.
On Friday we conducted a small activity where we looked at the spores of fungi and counted the number of asci that underwent crossing over during meiosis by observing their phenotypes. We then used chi-square to determine if our observed abundance could accurately support Olive's map distance theory which used mathematics to predict the expected ratio of crossed to non-crossed spores. My data ended up in support of Olive. We also watched a Vodcast teaching us about Chromosomal abnormalities, the various changes to genetic make up and the resulting effects as well as a few of the more prevalent genetic disorders and how they are caused such as the Trisomy of Chromosome 21 that causes Down's Syndrome. 

Monday, March 20, 2017

Examining Cancer Patient Data

This activity taught me that there are many different gene mutations that can lead to the same type of cancer. The mutations may be in oncogenes, tumor suppressor genes, they may be on chromosome 3, or even the X chromosome. Another trend I saw was that it appeared that in all cancer patients, be it hepatic cancer or other, the patients had at least two different mutations. This would lead me to believe it takes more than one mutation to cause cancer. The final thing I learned from this activity is that there are only 9 genes associated with genome maintenance. This leads to cell fate and cell survival being far more prevalent than genome maintenance.
It surprised me to learn how spread apart all the cancer genes appeared to be, even among patients of the same cancer type. There was almost no rhyme or reason to their placements and it seemed equally likely that a gene may mutate on any of the chromosomes. Likely this is why cancer has remained a mystery for so long, it's hard to pinpoint or predict and therefor hard to control and cure. As well it surprised me that no gene could code for more than one type of cancer. One thing I still wonder is a piece I mentioned earlier in observing that every patient had more than one mutation. Is that just a by-chance happening, or does one really require multiple genes to mutate before cancer develops. Or can an individual develop cancer by one mutated gene alone?

Sunday, March 12, 2017

Weekly Bio Journal #4 Mar. 12

This week we covered three new Vodcasts that centered around the Cell cycle. The weeks activities revolved around the information in those Vodcasts. Monday we filled out a POGIL on the cell cycle. Tuesday I was not in class because I had a Nordic State Meet race to attend. Wednesday we discoed the new Vodcast on the cells regulatory mechanics and worked on a corresponding POGIL. Thursday we hopped on the computers and completed an online HHMI informational program on the cell cycle and how it relates to cancer. Friday we had a shortened class due to the pep rally and spent class going over the information from the HHMI activity.
The information on the cell cycle came easy to me, I understand the order of events from G1, to S, to G2, to M. I completely understand the concepts of the checkpoints and the duties of each phase. I also can identify the order of phases in mitosis and identify them through a microscope. This week I learned what cancer really is and how it develops. The only road bump of the week is remembering the exact steps that the chromosomes go through in Meiosis. Its more complicated than mitosis as there are a couple more steps that ensure greater variation, but the terms like diploid and haploid when counting chromosomes and chromosome pairs gets a little confusing for me. I'll just have to review those sections and look over diagrams and illustrations to help me remember.

Saturday, March 4, 2017

Weekly Bio Journal #3 Mar. 4

This week back from February back, centered around one laboratory experience: PCR. After having learned about the Polymerase Chain Reaction and electropheresis in our 4.3 Biotechnology Vodcast, the class had the opportunity to have hands on experience with the technology. Everyone took cheek cell samples from their mouths, separated the DNA, and amplified the samples using PCR. The next day we practiced the delicate process of staining the DNA and placing the tiny samples in the fragile gel within the electrophoresis bath. This was a tremendous hands on opportunity to show us actual experience with working in a bio-lab doing the very things real lab technicians do everyday for important analysis and research. The next day we analyzed the electrophoresis results and measured the bands to see how much of the class was homozygous or heterozygous for the target gene. We then did some calculations to determine if the class was in Hardy-Weinberg equilibrium and compared our class results to other populations around the world.
By this point, through listening, recording, and hands on participation, I believe I fully understand the majority of the workings of PCR and gel electrophoresis. Enough so I could explain the process to make it intuitively obvious to even the most casual observer. During the lab however my DNA did not register in the electrophoresis. I messed up somewhere along the line during the lab work. I don't have a particular salivating mouth so I likely had a small spit sample to begin with. I had a very small pellet after the centrifuge and I believe I accidentally sucked up some of the small sample through pipetting later. This was likely the cause of my poor gel results. I just need a little more practice with this particular lab is all, likely a second run I would have produced results having already gone through the procedure once.

Sunday, February 12, 2017

Weekly Bio Journal #2 Feb. 12

This week on Bio Life, our intrepid hero Gridley braved blizzards and dreaded Mass drivers to receive his daily dose of Biology. He began the week by completing a Pogil on the translation of RNA into proteins. Because of how extensive the Vodcast was on this subject and because of my complete note taking this Pogil was fairly easy as I felt I had a firm grasp on the concept. As a result I feel I understand the Central Dogma. We next completed a packet on the impact of mutations that centered around the Myostatin Belgian Blue, a breed of cattle that due to a mutation in their genome have an inhibited production of the muscle inhibitor protein Myostatin. Animals with this mutation have double muscle growth and in the packet we analyzed several locations in the gene where a mutation occurred. Similarly we explored another packet on the mutation in pigment production of Rock Pocket Mice. Here we explored the affects of silent mutations, versus missense mutations, versus nonsense mutations.
Over the period of several classes we created and described the steps of transcription and translation using play-doh. Me and my partner used a genome sequence generator to select a DNA sequence 30 nucleotides long and using different colored play-doh, represented each nucleotide. We then made a 3-D model of the process of transcription and translation with the play-doh. At first we struggled to come up with an idea of how to represent the information using play-doh but once we got the ball rolling we set off like a spontaneous reaction.
At home I completed the three part 4.3 Vodcast on Biotechnology. This lesson was a little harder to digest than 4.2. I would like to know more about plasmids and how they work and exactly what they are. From what I gather they act as templates for altering genes or for producing clones. This lesson is very new because so much of this technology is so new and is in the very frontier of our biotechnology so I can understand if all the concepts are slightly slow to digest. I expect I will make sense of most of it come disco time next week.

Sunday, February 5, 2017

Weekly Bio Journal #1 Feb. 5

We have just begun studying our fourth unit (Information). This week coming down after the Midterm exam, we mostly focused on Vodcast 4.1 and getting through the dense and extensive 4.2 Prezi. 4.1 introduced us to the background history of the research process of our modern understanding of DNA. 4.2 focused on the Central Dogma: DNA into RNA into proteins. 4.2 covered replication of DNA, transcription unto RNA, and translation into coding proteins. We also worked in class on a argument project to determine using hereditary data, whether "Jeff" was related to the family he claimed.
 Overall I understood all the new concepts of this week and the new lesson. I owe this to the fact that the new Prezi was so extensive, being over 112 slides long, and the fact that I took almost equally extensive notes. At first the leading and lagging strands of DNA did not make sense to me and I did not see why lagging strands existed. However this confusion was fixed within a day when I "discoed" with classmates and returned to my notes at home. Even reading the data on Jeff's DNA markers for the argument project did not compute at first. But when I read through the evidence section of another classmates presentation, it was made crystal clear. It really helps to be able to discuss and share information with our peers.
As far as a connection to the context of the course, the information we're learning on DNA relates backwards to the very beginning of the course. DNA codes for the production of proteins and enzymes used in photosynthesis, the knowledge of bonds and structures from unit two explain the workings and directions of the DNA strands, and considering how colossal the amount of data there is to be processed and replicated it is far more comprehensible that mutations occur leading to natural selection of different genes.