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!  

Science, a Field of Imagination

“I’m not creative, so I think I’ll probably end up going into science.”  “Scientists are just robots.”  “Science is one dimensional, two at best, it doesn’t require creativity.”  “Scientists don’t have to think outside the box.”  

The common misconception that science doesn’t require creativity or imagination is inaccurate.  The word creativity often brings to mind artists and musicians, rather than scientists.  Artists paint on a canvas and musicians play instruments in an orchestra, both of which are perceived as “beautiful,” a word society links to creativity, while scientists must follow the scientific method and use measurements, graphs and statistics, none of which are typically thought of as “beautiful.”  However, while science and art may be different processes that produce different results, science does require the use of imagination and an ability to think outside the box.  

A common argument people cite when making the point that scientists aren’t creative is that science is procedural and the scientist simply follows the steps.  While this argument has some merit, it omits a very important piece: that the scientist chooses the procedure and the tools she’ll use to complete it.  This decision of how to collect data that will provide the best possible answer to a scientific question is difficult and requires creativity, as each tool provides the opportunity to collect different results.   It’s not unlike an artist who must choose whether deep, dark colors of oil paints or the monochrome, stark nature of rusted metal will best portray his message.  For example, when Alfred Hershey and Martha Chase were working to determine whether DNA or protein was the heritable genetic material of life, they had to brainstorm the best methods to go about doing so.  They used new tools, like bacteriophages and radioactive tagging, in a different way, transferring and tracking macromolecules.  They tried various methods, and used blenders in unprecedented ways to separate results (Lee, 2013).  They analyzed results, repeated the experiment and reanalyzed the results to ensure they were correct (Szybalski, 2001), and they found that DNA, not protein is the molecule of inheritance (Brown, 1970).   This thorough search for a procedure to yield the desired data is typical in science, and coming up with each idea requires not only immense knowledge and research, but also plentiful imagination and creativity.  

Once a scientist attains their results, the necessity for creativity continues--the message still needs to be communicated.  Similar to choosing which tools to use in conducting research, there is a plethora of statistical analyses available, and deciding which to use and how to use them based on the data and the goal of the experiment requires serious consideration and thought.  Continuing with the painting analogy, it’s like choosing which color oil paint to apply to the shadows of a woman’s face in order to bring out the sunshine lighting her icy-blue irises.  Should the painter use a deep brown with a red tint or more of a purple so dark it’s almost black?  In both the case of the artist and the scientist, the goal is to most successfully communicate one’s interpretation of the world.  Analyzing data can be especially difficult if they go against what one hypothesized and believed.  When a scientist’s experiment doesn’t come out as expected, first, the scientist looks into possible experimental errors, a process that requires one to be thorough and think of every possible error, usual and unusual.  Second, a scientist must be open, and realize that, while their data may not be related to what they were expecting, it still tells them something important, not unlike an artist acknowledging that a slip of their brush may not have ruined their painting, but simply changed the meaning.  This was the case with Griffith, when he was researching the possibility of creating a pneumonia vaccine using different strains of the bacteria.  He found results that didn’t pertain to the focus of his research, but was able to extrapolate from them an important discovery for humanity: bacteria can transfer their DNA (Griffith’s Experiment, n.d.).  Griffith had to be innovative and think outside of the box to interpret his unexpected results.  

Finally, scientists, like artists, face limits.  Whether these are a lack of tools available or a lack of funding, limits affect the ability of the scientist to complete his experiment as desired, and coming up with alternatives requires a great deal of imaginative thinking.  Dr. Shinya Yamanaka of Kyoto University, a major scientist in STEM cell research, had a multitude of difficulties with funding and space when he first started as a STEM cell researcher at Osaka City University in 1996 because he was a mere assistant professor.  He received next to no funding, was given a single seat in a shared laboratory to complete his research, and was not allowed to use embryonic cells in his work--the only way that anyone had conducted STEM cell research at that point.  But, not unlike the starving artist, he made do with what he had and continued his work.  Eventually, by being creative, Yamanaka worked around a lack of funding and materials and finally achieved a previously unfathomable goal: be able to conduct research of STEM cells without using embryos.  He accomplished this by reprogramming adult cells to revert back to STEM cells (Fackler, 2007).  While there is still much work to be done, as many of these reprogrammed cells turn cancerous, Yamanaka has taken the first step, and the rest can also be accomplished with further unbridled imagination and boundless hard work.  

Science, traditionally thought of as rigid, is not so uninventive.  Innovation and the ability to create are at a scientist’s core; without this mindset, science would not progress, just as art and music would not progress.  Science is considered unoriginal is thus uncreative, because it follows rules and builds off of previous research, but, in effect, so do art and music.  This is how humanity develops: by learning from mistakes and using and improving upon what works.  The next time someone says that science does not require creativity or imagination, correct them.  Help them learn that science, like art, requires full use of an innovative mind.  Remind them, in the words of Albert Einstein, that “The greatest scientists are artists as well.”  

Works Cited and Consulted:

Brown, T. A. (1970). The Human Genome. Retrieved December 16, 2016, from

https://www.ncbi.nlm.nih.gov/books/NBK21134/http://library.cshl.edu/oralhistory/interview/csh

/memories/szybalski-martha-chase/

Szybalski, W. (n.d.). Waclaw Szybalski on Martha Chase [Interview]. Retrieved May 11, 2001, from

http://library.cshl.edu/oralhistory/interview/cshl/memories/szybalski-martha-chase/ and

http://library.cshl.edu/oralhistory/interview/cshl/alfred-hershey/szybalski-hershey-chase-experiment/

Lee, R. J. (n.d.). Gender Bias in Science, Part IV: Martha Chase [Web log post]. Retrieved October 28,

2013, from http://www.themadscienceblog.com/2013/10/gender-bias-in-science-part-iv-martha.html

Griffith's Experiment. (n.d.). Retrieved December 16, 2016, from

https://education.llnl.gov/bep/science/10/tLect.html

Fackler, M. (2007). Risk Taking Is in His Genes. Retrieved December 18, 2016, from

http://www.nytimes.com/2007/12/11/science/11prof.html

More Efficient Than Nature

Wow, this, I guess like every other article I have read so far, is so cool.  I love the idea and concept of a bionic leaf, even if I have sliiiiiight PTSD from the photosynthesis and cell respiration unit--trying to keep all the details of each process straight and separate from each other was hard!  I am realizing that I definitely need a good refresher on all of that though, because when I read that the water-splitting molecule in this artificial process is an alloy of cobalt and phosphorus, my immediate thought was, how does that compare to the water-splitting molecule in natural photosynthesis?  But I couldn’t remember what that molecule is, or if we even learned what it is.

I found the whole idea of being able to take a natural process and tweak things to make it more efficient to be very interesting.  I guess the purpose of this process is different from that of natural photosynthesis--generating alcohol instead of ATP--but it seems like nature would want to be as efficient as possible.  So why isn’t natural photosynthesis more efficient?  Why is it that with a little (or maybe a lot) of messing with nature, scientists were able to make a process ten times more efficient?

Some of the other questions I had were more basic, like what does the bionic leaf look like?  I always find being able to visualize something to be helpful in remembering it, but there was no image of the leaf.  At first I was picturing a leaf that is bionic, but then read in the article that it is called a “leaf” because of its “melding of biology and technology.”  I figured the biology part was the whole idea of using a process similar to photosynthesis, and that it ended there, meaning it probably doesn’t actually look like a leaf.  But I decided to look it up on Google Images just to make sure, and in all the pictures I found, it looked like a little bionic leaf, just as I had originally imagined!  This leads me to wonder, where are these leaves going to be used in our society?  Are we going to start having artists make tree sculptures in cities so that these bionic leaves can be attached to them?  That would be cool!  Or would it be more productive to just make large panels and put them on the roofs of buildings and in fields, like we do solar panels?  If the desired end result of this leaf is alcohol that can be used for fuel, is it going to be produced in liquid form, because it would be at air temperature?  If so, where is the liquid going to be collected?  In little individual compartments for each leaf, or would there be a way to pipe it to one larger tank? I’m very curious as to how these leaves are going to be incorporated into society.

First of all, just because I thought this was great, I want to share how my dad picked up this article, read it, and then kept asking again and again whether I had read it yet.  I guess I know where I get my fascination with biology from!  Second of all, CRISPR sounds like something to do with keeping salad greens fresh.  It is obviously an acronym for something important and relating to the process, but still.  

Ok, now down to article.  The genetics unit was my favorite; I loved how everything went together, how everything to do with how we operate is encoded in our DNA, and how we are still making new discoveries every day.  It just amazed me--and still does.  It is crazy to me, but also at the same time expected, that we can now edit DNA.  (It seems like it would be possible when I think back to the way DNA is unwound and replicated that at some point during that time we would be able to go in there and edit the DNA.  I’m not sure that’s when this gene editing would actually happen, but that would be interesting to know.)  I was wondering when this time would come, but now that it’s here, it’s still hard to believe.  

This whole advancement is incredibly interesting (WE CAN EDIT THE MOLECULE THAT DICTATES WHO WE ARE, WHAT?), but I found it especially so that NYC researcher Timothy Chan says that taking cells from the site of the tumor specifically would improve the method’s effectiveness, as these cells would already specialize in attacking the cancer.  I guess that makes sense, but I would love to know more about why and how that works.  I also found it interesting how involved China is with anything to do with gene editing and how quickly the nation moved ahead with this project.  It’s honestly kind of scary, and I have to wonder how meticulous they were when looking into the safety of the process and the possible side effects.  

So yeah, it’s insane and awesome that we can now edit our genes to delete one and perhaps cure cancer, but I also have worries, and being a bit of an anxious person, these stand out to me.  The issue of editing DNA in the wrong place (apparently a “well known” danger--eek!) is taken care of, because the cells will be examined before being inserted back into the patient, but other problems have not been resolved.  It sounds to me like the PD-1 gene is responsible for preventing cells from launching all-out immune responses and killing healthy cells, and so the fact that the goal of this gene editing is to remove this gene makes me concerned.  Does this mean that our immune system will no longer have limits and will then go kill healthy cells?  Chan has also expressed his worries regarding this, that the immune system will attack “the gut, or adrenaline glands or other normal tissue.”  Would this happen instead of killing the cancer?  Alongside killing the cancer?  After the body has done its job and the cancer has been wiped out?  And since gene editing is passed on to the next generation, what kind of implications would that have?  Would this mean that the next generation’s immune system would not be controlled?  I can only imagine that wouldn’t be good.  

Along slightly different lines, another question I have is what other genes the U.S. will be using in their pending trials, as they said they will be using the gene for PD-1, as well as knocking another one out and inserting a third, and why they are using these genes.  

This is a scary process and I can’t help but worry about the possible negative side effects, but I think that this is largely the case with any new idea.  Of course there are going to be issues with it, but will they overwhelm the positive effects?  That’s what we have to find out, and it sounds like we will be finding out soon.