Reflection for Week of March 27-31

This week focused on diving deeper into genetics and patterns of inheritance, and solidifying our use of Chi Square Tests with respect to genetics (4.5-4.10).  We began Monday with our big fruit fly virtual lab, and continued it into Tuesday and Wednesday.  This dealt with largely basic Mendelian patterns, as well as X-linked genes and homozygous fatal phenotypes (4.5 and a bit of 4.6), and was my favorite part of the week (although the simulation of the flies hatching really grossed me out).  This lab was largely review of material from sophomore year in a new setting, but we also learned lots of new material this week via vodcasts.  Vodcast 4.10 dealt with extending our understanding of how traits can be expressed and passed down, with patterns like epistasis and pleiotropy, as well as penetrance and expressivity.  Vodcast 4.11 focused on human genetic conditions like Tay Sachs and Huntington’s, and whether they were autosomal or sex-linked, and dominant or recessive.  Vodcast 4.12 focused on gene regulation in prokaryotes and eukaryotes, and how this leads to differentiation in eukaryotes and efficiency in both pro- and eukaryotes.  

I think I did well with the material this week.  I understood the fly lab, and really enjoyed trying to figure out what kinds of traits I was dealing with.  My Cross #4 was rather disappointing, however, because it was the same X-linked recessive pattern as Cross #3.  I had to cut my loses though, as I was running short on time this week.  That seems to have become a prevalent theme in my life.  Anyway, I also feel pretty good on Vodcasts 4.10 and 4.11, but 4.12 was almost entirely new material and was a doozy for my brain.  I think with some serious looking over, Mr. Anderson videos, and questions for Mrs. Cole, I’ll feel good with it next week.  I also felt very good on the majority of the Genetics Problems Set #2, but I definitely need to wrap my head around the whole gene mapping thing a little better.  Based on Mr. Anderson’s video, I thought that all the frequencies would add up exactly, but then they didn’t, so I was confused for a bit.  It makes more sense this way though, as I was having a hard time seeing how frequencies could be translated directly into distances.  I will look at the fungus lab again tomorrow, as I think that will also help me understand gene mapping.  

As I said last week, the purpose of DNA is to code for the genes that comprise us, and with the material this week, we now know the majority of our traits are not Mendelian.  Understanding how genes are expressed and what acts on them (parents, environment) is key to understanding how populations evolve and are acted upon, as was studied in Unit One, how the body synthesizes the proteins, carbs, lipids, and nucleic acid as discussed in Unit Two, and how our body is able to create and store energy, as was looked at in Unit Three.  Because of how important genes are, gene regulation is absolutely imperative to understanding life.  This is how we get different organisms, how we don’t all look the same, how we change over our lifetimes.  This is a field that is incredibly relevant right now (not that all of biology isn’t), and that makes it so, so interesting.  We never know what we might learn next.  

Reflection for Week of March 20-24

This week was all about getting back to basic genetic patterns (4.2 and 4.5), like Mendelian Genetics, and codominance (blood type and sickle cell disease).  We went over the basic terminology, like heterozygous, homozygous, dominant, and recessive, and began using Punnett Squares again.  Most of this was review from sophomore year, like generic monohybrid and dihybrid crosses, but some of it was new, like the way we learned to do dihybrid crosses by multiplying probabilities rather than making a four by four Punnett Square.  This new trick was SOOOOOOO incredibly useful, especially since we can now do, say, tetra-hybrid crosses (no, you don’t want to make a massive Punnett Square, as it turns out!).  We also dove back into Chi Squares, and while I still have some questions about the technical side of what exactly I’m looking at, not having taken Stats, I get the basic idea and can use them to analyze data.  Our last activity of the week was the fungus tetrad crossing over activity, and wow, fungus is weird.  I was very confused as to what I was seeing, but with some questions for Mrs. Cole, I mostly understood the strange lives of fungus and the activity made more sense.  Fungus are still weird, though.  

Overall, I feel pretty good about this week’s work.  Much of it was review, and it was good to get back to genetics, but even the new material wasn’t hard for me to understand, probably because there wasn't a ton of it for me to process.  I think I would like to take one more look at the fungus lab and really thoroughly take in the lifecycle of fungus, because it is so different from ours and I would like a more solid understanding of it.  I also need to work on my understanding of Mendel’s Laws of Segregation and Independent Assortment, as I feel a little rusty on those and where they are reflected in meiosis.  I will take another look at those, and come to Mrs. Cole with any questions I have. I would also like to better understand Chi Squares, but that is time-dependent.

Coding for genes and alleles is the purpose of DNA, so fits nicely into our information unit.  Understanding how genes are expressed is key to understanding how populations evolve and are acted upon, as was studied in Unit One, how the body synthesizes proteins, carbs, lipids, and nucleic acids, as discussed in Unit Two, and how our body is able to create and store energy, as was looked at in Unit Three.  Without genes, what would we be?  Wow, that’s a question my brain can’t even handle right now.  I’m going to stop there.  

Cancer Activity Reflection

• Three things I learned from this activity.  
• There isn’t a set formula for cancer.  Even within a single type of cancer, like leukemia, different genes and different numbers of genes can cause uninhibited cell growth that result in tumors.  
• There are some chromosomes that contain more genes responsible for cancer than others.  In my groups, chromosomes 7, 9, and 17 were the main sources of cancer genes.  
• Scientists have split cancer genes into three categories based on their functions: cell survival, cell fate, and genome maintenance.  We had discussed whether genes were oncogenes or tumor suppressors, but we had yet to learn what the functions of those two types of genes were, and how their functions would play into them causing cancer.  
• Two things that surprised me.  
• I was surprised that there were so many different ways to get a single type of cancer.  I had never really thought about the steps that the body goes through when it begins to have cells proliferate uncontrollably.  Once we started learning about cancers and I began to understand that multiple genes are usually involved in development of a cancer, I thought of it similar to the one-gene-one-enzyme idea: each type of cancer is produced by a single combination; there is only one way to produce each cancer type.  The truth is, there are multiple ways for a cancer to develop, different combinations that will lead to the same type of cancer.  
• One question I still have.  
• I am still, naturally, wondering how each of these genes operates specifically.  What part of the cell cycle do the play a part in?  Why does a mutation cause cancer?  I am curious about the pathways for each of these genes, even though it is unrealistic to learn about each of these with my lack of time.  But I might research at least a couple of them, perhaps the three I had on my leukemia card.  

Reflection for Week of March 6-10

This week was focused on moving forward in Unit Four, specifically in cell division.  We learned the phases of the cell cycle, the phases of mitosis, the hormones and enzymes that regulate if and when a cell goes into mitosis and divides, and began looking at meiosis, the process by which gametes are formed in sexual selection (4.4).  This week was probably one of the busiest of the school year for me, and so, considering that, I think I did pretty well with the work.  For homework, we had three vodcasts in Unit 4 to complete, as well as our PCR lab write up.  This was a bit of a struggle for me, because I spent a lot of time trying to make sense of and organize all the material from the lab to ensure I included everything I needed to and made sense while doing so.  Because of this, I wasn’t able to concentrate on the vodcasts as well as I would have liked to.  Usually, if there is something in a vodcast I don’t understand, I won’t move on until I have rewatched it or searched out other material in the textbook or online to help me understand, but with my time being so limited this week, it was all I could do to get the vodcast done and make sure I understood enough to answer the WSQ questions.

We began the week by completing Vodcast 4.5 as homework.  It dealt with the phases of the cell cycle and mitosis, and reviewing the terminology associated with cell division, like chromatids vs. chromosomes, centromere, and diploid vs. haploid.  I feel pretty comfortable with all of the material in 4.5, as it is largely a review of Adv. Bio, but I will work on solidifying everything, since I didn’t get to take as much time on the vodcast as I usually like to.  Among new things mentioned in this vodcast were  1) the addition of “Prometaphase,” a little in-between phase where the chromosomes begin to migrate to the center of the cell and two complete spindles have formed, and  2) a small section of the evolution of mitosis that discusses that there are more similarities between eukaryotic and prokaryotic cells that we usually think.  I think I have a good handle on these two new additions, and find them interesting!

Our second vodcast of the week was 4.6, which dealt with regulation of the cell cycle.  This is a brand new subject for me, and so I am still feeling a bit uncertain of the specifics, such as which checkpoints are responsible for what, and which hormones and enzymes they employ.  What has helped me feel more familiar with this new material is the work we did with the HHMI packet.  I still definitely need to spend some more time straightening the specifics though.  

Our last vodcast of the week was 4.7, a review of meiosis, complete with that earworm video of the chromosomes doing do si dos.  That has literally been stuck in my head all weekend.  Anyway, Vodcast 4.7 reminded us what meiosis is, the stages it has to go through in meiosis 1 and 2, and the cell’s progression with regards to being haploid and diploid.  One part that we had gone over to an extent, but never this specifically, was how many different gamete combinations are possible.  Seeing those numbers was insane, and really made it sink in how incredible meiosis is.  I mostly understand everything to do with meiosis when I’m looking at the information, with a few questions on the whole haploid-diploid piece, but I definitely need to spend more time so that I can remember things without having to look at the paper.  I think I should be good by simply watching the vodcast again, but if that doesn’t do it, I’ll see if there are any good Khan Academy videos or other online resources, or, of course, ask Mrs. Cole.  

Cell division is imperative for life to sustain itself as an individual organism and as a species, so our work this week was crucial to our understanding of biology.  Organisms need to heal and grow, so mitosis is important to the survival of individuals, which is important to the survival of populations.  Regulating mitosis can mean life or death, because of the mutations that can be passed down affecting tumor suppressors and/or proto-oncogenes.  Meiosis is how sexually reproducing organisms are able to continue their lineage and sustain a population or species, and is the reason that we sexually reproducing organisms are all so different.  Without these processes, regulated by enzymes and hormones, we wouldn’t have the organisms we have today, nor the variation that is present in them, allowing mechanisms of evolution to act upon populations and shape them.  

Reflection for Week of February 27 to March 3

Ok, so this week, things are going to be a bit shorter, as I am feeling rather burned out and like my brain is slowly dissolving inside my head.  Why isn’t it still vacation?  

I think I did pretty well with the work this week.  Monday we discoed Vodcast 4.4 on viruses (Domain 4.3), which I feel like I have a pretty good handle on given that I accidentally studied them for the quiz on Friday.  There are still a couple of questions I have, but nothing major.  For example, I really want to know how viroids causes disease, but, as it turns out, biologists don’t know that for sure yet (or even close to for sure, since you don’t ever really know anything “for sure” in bio).  

The rest of the week was spent on the lab (Domain 4.1, and, more importantly, my favorite part of the week!), which I feel like I understand the process of well, having completed the online lab, read the prelab thoroughly, and done the lab.  What I’m not so sure about is the whole database analyzation piece, but I’m sure I’ll have a better idea after talking to Mrs. Cole.

On Friday we had a quiz, and, after studying for it, I feel like I have a pretty good handle on the biotech tools, applications, and ethics, which I was feeling overwhelmed about the last time I wrote a reflection.  The ethics part is a difficult one, because it is personal, and I am someone who likes to take my time processing information and exploring different beliefs to understand what I myself believe.

I think I can definitely improve when it comes to understanding the analyzation part of the lab, having missed Thursday.  I feel overwhelmed right now, and am unsure how I am going to finish it by Wednesday. But I will keep working steadily and see where that gets me.

The lab largely had to do with PCR and electrophoresis, two common tools of biotech, and fits very neatly into the curriculum.  We learned about biotech tools leading up to vacation, and, in order to understand how these biotech tool work, one must understand how certain aspects of biology, like DNA replication in the case of PCR, and restriction enzymes and DNA structure in the case of electrophoresis.  

Reflection for Week of February 6-10th

This week focused on solidifying standards 4.1 and 4.2, and beginning to cover biotechnological tools and their applications and implications.  I started out the week feeling a little confused, what with having rushed through Prezi 4.2, but I spent time going over the Prezi again and watching Crash Course and Bozeman Science videos, and that helped clarify the majority of the material.  The questions that I still had, I asked Mrs. Cole and she, as usual, cleared up all my confusion!  I feel pretty good on replication, transcription, and translation now, although I still often have to pause and think about what details belong to what process.  What helped me remember this was the play-doh fun we had!  Having made some proteins, like RNA polymerase, and not others, like DNA polymerase, helps me remember which enzyme is used in which process.  I also felt good on the POGIL, the Schwarzenegger cow (if the mice are Schwarzenegger mice, then the cows should be Schwarzenegger cows), and Rock Pocket mouse packets, and I didn’t go down a rabbit hole about how the change in the DNA signals different amounts of pigment in Rock Pocket mice, like Kirk and I did when the cute critters were introduced to the class in Unit 1.  I’m still in awe about how much of a difference a single point mutation can make!  

I’m feeling pretty good on the material from 4.1 and 4.2, but 4.3 threw me for a spin.  I either really get a biotech tool and can see how it could be used immediately, or I have no idea what it is or how it works; there doesn’t seem to be an in between.  I generally understand the tools that I have worked with, like restriction enzymes, PCR, and gel electrophoresis.  I also think I have a pretty good understanding of sequencing and gene libraries, although I want to feel a little more solid on them.  I do not understand vectors (I have no idea what these are, and I feel like I am probably overthinking it), labeling (I get the overall idea of this, but not the specifics), and microarrays (I thought I knew what was going on, and then turns out I didn’t at all, which was an unfortunate realization).  In general, I feel like I understand the applications better than the tools themselves.  

I was feeling similarly lost last week about the 4.2 material and I now understand it, so I have no doubt I will get biotech tools and applications. It will just take time.  Unfortunately, with this material, there aren’t any Crash Course videos, and the one Bozeman science video is about all the processes I feel ok on, naturally.  But I will watch the vodcast again, now that I have had some time away from it, and I will ask Mrs. Cole--you guessed it--more questions!  And don’t worry, I promise there will be no flashlights!

Anyway, my favorite part of the week (I think I will make this a theme in my reflections) was playing/working with Play-Doh, which we did Thursday and Friday.  I love making things and learning, so this was basically heaven.  I worked with a partner that I don’t think I have ever worked with (sorry Naomi, I can’t even remember what day yesterday was, so don’t take it personally), and that was a lot of fun.  I feel we worked well together, shared a practical mindset when it came to the project, and used our time wisely.  This may be the first time I finished my work before a lot of my friends (gasp!).  

Basically our work this week focused on furthering our knowledge about our genetic blueprint, how it functions to create who we are, and how we can alter that.  This, of course, is a very important part of the curriculum, and it has connections everywhere.  Alter a protein and you alter its function, which may be to create or destroy other molecules that we learned about in our matter unit, or it may be to create ATP, a molecule we discussed in our energy unit.  Genes are the material of natural selection, so this unit has everything to do with Unit 1.  Unit 4 gives rise to everything discussed in the other units, and I really look forward to fully understanding and expanding my knowledge on the tools that we can use to alter the molecule that makes us who we are.  

Reflection for Week of January 31-Feb 3 2017

Standards 4.1 and 4.2

This week was all about the introduction of the role that information plays in life.  Domain 4, Information, deals with DNA, RNA, protein synthesis, expression of genes based on genotype, and how mutations affect this, and this first week gave me a taste of everything.  

We started the week Vodcast 4.1 as homework.  This dealt mainly with the history of DNA and how experiments built off one another, as they do in the scientific community, to get us to understanding of genetics that we have today.  I feel that I understand these experiments, such as Griffith’s vaccine gone wrong and Hershey Chase’s exceptional use of radioactive tagging.  I think I understand them well because I learned about them in sophomore year and also wrote about them in my essay arguing for the creativity of science.  The one experiment that I didn’t feel completely comfortable with was TH Morgan and company’s contribution to the understanding of inheritance.  

My favorite parts of the week were some of the packets we did.  I liked the Meselson and Stahl packet where we followed the scientists' line of thinking to determine that DNA replicates semiconservatively.  I always like when we do a packet that has us reason out why something is the way it is, because I am less likely to forget the concept.  My favorite packet this week was the one where we used genetic markers to determine whether Jeff could be related to the H. family, because who doesn’t love a good mystery?  

I had a hard time with Prezi 4.2, largely, I think, because I felt rushed when I was doing it.  This meant that when I didn’t fully understand something, I didn’t take the time I should have to look it up, or at least look at the slide for a little longer.  I get the broad idea of replication, transcription, and translations, and the POGILs helped with this, but am shaky on some of the specifics, such as the proteins involved in replication, what transcription factors are exactly, and the sequence of events in these processes.  Also, I do not really understand Beadle and Tatum’s experiment.  

This shakiness, I am sure, will get better once I have a chance to sit down with the material for a while.  That will be my starting point in bettering my understanding, but I will also look at other sources, such as the Adv. Bio vodcasts (I like the combined visual and audio, and I also feel that I don’t really understand these Prezis very well), the textbook, and the videos by Mr. Anderson and Crash Course Biology.  Lastly, I will, of course, interrogate Mrs. Cole with all my remaining questions! :)

DNA is the blueprint for life, and so is obviously a very important part of the course.  This unit basically explains the how and why of the cell’s workings: how and why DNA, mRNA, and tRNA are structured the way they are, and how this dictates the way the cell operates, that sort of thing.  DNA’s ability to replicate, be transcribed and be translated is the reason that the cell operates the way it does, the reason that we can inherit information from our parents, the reason that proteins are produced, and why certain proteins are produced in certain cells.  This unit connects to our first unit on evolution, because evolution is based in genetics, our second unit on matter, especially the organelles section, and our third unit on energy, because many of these processes require energy.  In regards to unit two, it has been fun for me to remember how some of the organelles that we learned about in unit two function together to accomplish what needs to be done by the cell.  For example, how the ribosome, when it creates a special “signal peptide,” goes the RER and creates the rest of the polypeptide there.  I’m not exactly sure why or how that happens, so I guess that’s another thing I need to clarify!