Learning Journal 1
Learning Journals are a tool commonly used in professional schools (medical school, nursing school, teacher college, etc.) and in the humanities both to help learners engage in metacognition and to help instructors evaluate students’ learning.
Think about the work you did for BIOL463 so far (in and out of class, formally and informally), then try to address each question to the best of your abilities. You can then copy and paste your answers into a Piazza, Facebook or wordpress post.
1. Factual knowledge
Briefly describe one new piece of factual knowledge that you acquired or developed since the start of the course.
Totipotent is a term used to describe the ability of one cell to develop into a complete organism. In the case of the cloning experiments discussed in the reading it is the ability of the nucleus of one cell to generate an entire organism when placed inside the oocyte of a different organism. Interestingly, when this process is performed with cells that have become more specified in their function, they lose their totipotency. I was not aware of these experiments prior to taking this course.
2. Making connections (conceptual knowledge!)
How does this new piece of knowledge fit into what you already knew? What other facts is it connected to, and how? Does it fit into any concepts? How?
The readings explained that the ability of oocytes fertilized by somatic nuclear transfer to generate a complete organism was initially used by geneticists to validate the theory that genes were the driving force behind for the changes seen during development. Years later we now know more about how gene expression drives these changes and often take for granted the effort that went into initially proving that it was in fact the nucleus and not the cytoplasm that proved to be the more important factor in explaining how changes occur during development. Proving that genetics play an important role in regulating development has allowed for more discoveries regarding the specific mechanisms that regulate gene expression and allow for cell specificity and in this way, the somatic nuclear transfer experiments can be connected to other concepts such as chromatin remodelling, in that they can offer an explanation for why we see a decline in the totipotency of nuclei that are extracted from cells that are produced later in development. The reasoning behind this would be that at least some of the genes that are necessary during the earlier stages of development are deactivated in cells that no longer need those genes. A skin cell wouldn’t need all of the genes that function in a developmental capacity and so said genes would be deactivated in skin cells. If the nucleus of a skin cell was transferred to an oocyte we wouldn’t expect the resulting cell to be totipotent as a number of the genes necessary for development would be shut off.
Learning Journal 2
1. One new (or ‘improved’) concept
Now that you have seen a variety of models for how enhancer elements work, different ‘flavours of enhancer elements’, the effects and characteristics of boundaries/insulators, the world of morphogens, common techniques, and possibly much more, identify and briefly describe one concept that is either new for you, or that you understand better or in a new way.
I found the section of the course on enhancers to be particularly interesting as I have been taking a biochemistry course that discusses similar ideas, just on a different level. Where biochemistry seeks to study the particular interactions between genomic DNA and proteins on a molecular level, Biology 463 takes a broader look at the subject and describes the role enhancers play in causing disease (enhanceropathies) or how they are specifically organized so that they may influence cell differentiation. The papers provided as background reading for the class provided me with a lot information regarding specific types of enhancers as well as a more in depth look at how they are organized into the genome in terms of spatial location. Prior to this, biochemistry 410 had only really discussed these in a general sense, in that they describe specific protein interactions that allow for the activation of gene transcription. So it was interesting to look at enhancer regions in terms of specific examples of their function ie “This specific enhancer functions in this way to activate this gene” rather than just discussing the general concepts that underlie how they function in terms of biochemical interactions such as protein-protein or protein DNA interactions.
2. Thinking about your new or ‘improved’ concept
- How did you identify your new or ‘improved’ concept? How did you decide that it is a concept (and not, for example, a fact or a skill or a technique)?
The overarching theme of the lectures and papers on cis-regulatory sequences was that there are DNA elements that can act on genes to regulate their transcription. As with many of these concepts one can use it to generalize a much more complicated issue. For example now I know that there are many different types of enhancers (shadow, fail safe and super-enhancers just to name a few) in addition to other regulatory regions such as insulators. There is too much information in this topic to properly distill it down to something like a fact. I have always seen techniques or skills as something that is applicable elsewhere or useful for determining something else. A concept is something that represents the idea that the techniques are based on. Take for example the 3C techniques. These techniques are based on the fact that enhancer elements form loops so that they may interact with the gene that they regulate. This technique takes advantage of an aspect of cis-regulatory regions to learn something new about them.
- That made you realize/decide that you understand it better or in a new way?
I was thinking about the overlap between this course and my biochemistry course. They both happened to be discussing different aspects of the same concept. Biol 463 is very focused on the overall result of regulation by enhancer regions and how this may influence development, whereas bioc 410 is interested mostly in understanding how transcription occurs and all of the proteins and DNA sequences involved in making that happen. I find it interesting that there is a disconnect between the two courses even though the underlying concept concerning cis-regulatory elements is essentially the same.
Do you think having a good understanding of this concept is important and/or useful? Why/how?
I think that exposure to different aspects of the same concept is important. Sometimes biochemistry gets too far away from the biological function of the proteins that they are actually studying. However on the other hand, the contribution of chemistry to biology is undeniable. Take for example the PCR technique. That is a technique that takes advantage of the chemical nature of DNA base pairing to allow for the artificial amplification of a sequence of DNA. Considering this I feel that knowledge of both is important to facilitate a greater understanding of the concept as a whole. An understanding of how a protein binds to DNA is for example useful if one wants to mutate it to see what effect this has on overall cell function.
Learning Journal 3
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Two things that stood out |
Type of knowledge |
What makes these things stand out for you |
Evidence/how you would test someone on this (select one “thing” only!) | |
| 1 | The Brison et al. article on Hox genes stood out to me. What struck me as being particularly odd is the spatial relationship between gene location and the expression of said genes. For example, the genes at the 3’ end of a cluster are expressed in the anterior and the 5’ genes are expressed in the posterior. | I would say that this knowledge is conceptual, in that it seems to encompass an aspect of how Hox genes seem to organize themselves inside their cluster. This is an idea that can be used to describe the organization of other Hox genes, rather than being a fact about where a specific gene is located within the cluster. | For me this stuck out because it seemed like an odd correlation, I did not expect the genes to be so well organized. I always expect biology to be “messy” and not to adhere to patterns that are so easily identifiable. So that there was a correlation between these two things seemed so odd that I thought I might have just misread the paper. | Since this is knowledge regarding the nature of Hox gene organization in general, students could be given information about the expression of a set of Hox genes in a mammalian embryo. You could then show them mutations in several of the genes and where these mutations affect the organism. Based on the given information, they could decide where the various Hox genes are located in the cluster based on the mutant phenotype. If they know about the spatio-temporal nature of Hox genes then they should be able to line the various Hox-genes up 5’ to 3’ within the cluster based on where the phenotype is expressed. For example, if the mutation occurs early and anterior then it will be closer to the 3’ end of the cluster. |
| 2 | I found the section on enhancers to be interesting as well. What stood out for me in particular was that that genes that are often regulated by a number of enhancer regions.
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I feel that this is conceptual knowledge. It is knowledge regarding the nature of enhancer regions and can be used to describe enhancer regions in general. Furthermore, it is an idea that concerns how enhancers are organized, rather than being a fact about a specific regulatory region. | This stood out to me just because of the sheer complexity of it. Prior to learning this I held a rather simplistic view of enhancer regions and how they function. I could imagine a single enhancer acting to regulate the expression of a single gene, when in reality there could be many enhancers that are potentially acting on this gene over a great distance to help fine-tune this gene’s expression at various stages in development. |
Learning Journal 4
- Name of the classmate whose portfolio you will be viewing:
Garry Bains
Browse through all the viewable parts of your classmate’s portfolio.
2. Imagine that you did not know this person at all, and you had to evaluate their skills, knowledge and learning using only the content of their portfolio. What would you say the biggest strengths of this person are, and why (what evidence did you use to come up with the answer)?
I think that the portfolio shows that Garry has a lot of interest in developmental biology. The “if I were a developmental biologist/geneticist…” post demonstrates this well. The ideas presented here have very interesting implications for the future of developmental biology and humanity in general. To me this indicates that Garry has considered what research in that area could potentially lead to, which is an indication of the interest that he has in the subject. This also indicates that he has done research into the subject, with regards to the development of the myelin sheath and the role it plays in the development of multiple sclerosis. This also shows that he is knowledgeable in the subject. The learning journal posts are also very specific in indicating the concepts that stuck out most to him. The post on the Hox genes demonstrates this. It does well to illustrate the main points regarding Hox gene regulation with going into too much extraneous detail.
In reality, you do know this person (at least enough to ask to see their portfolio!). With this knowledge, suggest how your classmate could demonstrate her/his skills, knowledge, or learning even more effectively in their portfolio.
In terms of learning demonstration, more explanation could be provided in some of the sections of the learning journal posts. More specifically, more explanation could be provided when explaining why certain information is conceptual as opposed to other types of knowledge. (I don’t know why the font is different here….)
3. I think that the biggest difference here is the amount of content in the learning journals. Otherwise the portfolios were fairly similar, although I added in the post about the adventure gene when I was thinking about unprompted posts that I could add. After reading Garry’s portfolio I feel like that the detail I put into some of my learning journals was perhaps a bit excessive. I think I went off on a tangent in a couple of the learning journals. For example in Learning Journal 2 I went off on a tangent about the similarities between biology and biochemistry and maybe that got a bit off topic. At the same time though I like to use the blog as a place sound off on some of the things that I have been thinking about, so I don’t really regret adding the extra material. I think it was worth it even though I did go a bit overboard.
Learning Journal 5
You are now almost at the end of your BIOL463 ‘adventure’… Congratulations!
There is one more Learning Journal to complete; try to address each question to the best of your abilities. You can then copy and paste your answers in your wordpress blog. Please do not build a new page, but rather add this LJ above or below your LJ1 entry.
1. And the most important thing is…
If someone asked you, ‘What is the single most important thing that you learned in BIOL463?’ what would you answer and why? (No cheating: only ONE thing!)
I think the most important thing that I learned in Biol 463 was that it changed the way I look at scientific papers. In spite of all of the material we covered regarding HOX genes, lncRNAs and other genetic regulatory mechanisms. I feel like a lot of the course was taught through analyzing figures from papers and discussing questions related to them. Because of this, I find that I look at papers differently after having scrutinized them in detail in class. I think that I understand more about the way in which they are organized now. I almost look at them as stories now, in that things happen in a sequential order: “We saw A in this experiment, so next we looked at B” and so on. Some of these papers almost have a sort of narrative quality to them in that respect. In some cases they found something interesting, this then leads them to attempt to tease out more about the underlying mechanisms behind why what they discovered acts the way it does. One thing leads to the next and this discovery fuels further research later on. I think that was the most important thing I learned. All of the factual and conceptual information provided by the course was interesting and I learned a lot about genetic mechanisms that I had not heard about before, take for example imprinting. But I feel like this cannot be applied elsewhere quite as well as the knowledge that I gained from reading the assigned papers and working through them in the in-class assignments. I feel like this taught me a lot about how to think about and analyze scientific literature (at least in the life sciences) and if I manage to make a career in science in some capacity, this knowledge can be applied to a great many things, perhaps even some that I haven’t thought of yet.
2. Your example of Taylor’s model of the learning cycle
Below is one of the many models of the learning cycle (in humans). Can you apply it to your own experience as a learner? Do you remember situations where you experienced the stages presented in the diagram? What was it like? How did you progress from one stage to the next?
Please address this question for two different contexts, one of them being BIOL463 and the other being any context you want outside of school.
I feel like I had a lot of “Whaaat?” moments in Biol 463, but the most memorable of them has to be when we were reading the Plank and Dean paper on enhancers. I read the paper through the first time and felt like I didn’t totally understand what was going on, there were so many examples and different enhancer functions that I found it hard to really get a lot out of it at first. It didn’t help that I thought that the questions were actually due in class the next day. I was kind of panicking at that point. That would be the disorientation stage. I actually got a bit obsessed with it and ended up reading it a couple more times before I could start to make out the concepts that were being addressed in the paper. This would be the exploration stage, where I worked at figuring out the examples. Answering the questions helped me to better assess the information and got me towards the reorientation and equilibrium stages of the Taylor cycle.
Outside of school, I like to play the guitar and I find this cycle sort of applies to the effort involved in learning a new song. When I have the time I like to try to teach myself to play songs by ear as a sort of challenge. I will initially listen to a section of a song and try to find notes that work alongside it. This would be the disorientation and exploration stage. If something doesn’t fit I will listen to it again and try something else. Eventually I will find something that fits with what I am hearing in that passage of the song. I then work with that to fine tune it. I know that there are parts of what I am playing that sounds right and other parts that don’t fit quite as well. This would be the reorientation stage. I then work with this until I am reasonably happy with it. At that point we have reached the equilibrium stage. So this is kind of like the Biol 463 scenario, except I am not being evaluated on how accurately I play a song, so in that way it is much less stressful.
Reflection/Comment:
The learning journals proved to be an interesting exercise in actually assessing what it was exactly that I have learned, which is something that I have not done in any of the other courses that I have taken. Before I go about assessing the information in each of these learning journal entries I would just like to point out that in assessing what I have learned by writing these learning journals, which are a form of meta-cognitive learning themselves is so self-referential that it makes my head spin.
I think that in performing these learning journals I was forced to consider what I had learned in a different light, in that I for the first time I was actually assessing what I learned and how it relates to other pieces of knowledge that I have already obtained. I also found that they provided me with a way to express my thoughts on the topics that we learned in class, in a way that didn’t necessarily need to be formal. In the end I feel like they provided a good outlet for my thoughts in certain topics related to the course material.
Learning Journal 1: Comments
Here I looked at the role of totipotency as discussed in the first assigned readings. I think that by writing this I helped to affirm my knowledge of the reading and also to consider the readings in terms of other aspects of the course or at least other pieces of knowledge that I had obtained from other classes. I think that this helped me to combine some of this information together in a way that I might not have though of otherwise.
Learning Journal 2: Comments
Here I was allowed to think more about the “continuum” that exists between biology and chemistry, I don’t know if I learned that much here in terms of the course material, but I think it gave me a place to think more about that idea. So I think it was ultimately an interesting thing to consider, even if it isn’t entirely relevant to the course.
Learning Journal 3: Comments
I feel that this journal gave me an opportunity to think more critically about the hox genes and the spatial relationship between 3′ to 5′ gene distribution and the anterior and posterior locations of the mutations. This allowed me to think about what kind of knowledge this was and also helped me to solidify that knowledge by allowing me to develop a question about it.
Learning Journal 4: Comments
This journal was more of comparison than anything else. Interestingly, it allowed me to assess someone else’s learning rather than just my own. I think it taught me a bit about how I might go about assessing someone else’s learning. Who knows? If I ever go into the teaching field, perhaps this will be useful to me.
Learning Journal 5: Comments
This journal taught me a bit about the learning process itself. It went back to the first day of class where we discussed this idea a bit. It caused me to assess my learning in other areas besides school and allowed me to see that that particular model of learning can be found in a great many examples of human learning.