Summer 2019 - Journal Club
For suggestions/ideas on papers to lead a discussion on, see our paper suggestions page.Schedule
May 24 - The antiquity of RNA-based evolution - Alex
Paper: Joyce, G. F. (2002). The antiquity of RNA-based evolution. Nature, 418(6894), 214–221. https://doi.org/10.1038/418214a.
RNA World Hypothesis
RNA World - a hypothesized era on Earth where genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA.
- RNA had the dual role of acting as a blueprint and construction worker for life (Banzhaf and Yamamoto, 2015)
- Contrast with DNA-replication: DNA = blueprint, proteins (and RNA?) carry out the construction work
Figure 1 from (Joyce, 2002)
(Joyce, 2002)’s RNA World Story
- Chemical building blocks for RNA-based life that may have been available in the pre-biotic environment:
- amino acids, hydroxy acids, sugars, purines, pyrimidines, fatty acids
- These building blocks combined to form polymers (polymer = large molecule, composed of many repeated subunits)
- Some polymers may have had special properties: e.g., adherence to surfaces, resistance to degradation, tendency to form large aggregates
- Eventually, though, all of these types of polymers with special properties would have succumbed to degradation
- If polymers capable of giving rise to copies of themselves arise + the rate of self-replication > the rate of degradation of existing copies: that self-replicating type of polymer is able to persist in the environment
- A changing environment would have selected for general purpose (more robust) replication machinery (e.g., RNA replication machinery)
Each of those bullets and the transitions from one to the next are wrought with open questions.
Some open questions (as of this paper)
- What are plausible mechanisms for the emergence of RNA from the ‘prebiotic clutter’?
- I.e., How feasible is RNA formation under prebiotic conditions?
- What would the first RNA replicators look like?
- Possibility - template-based replicators
- Possibility - Autocatalytic network of ribozymes
- One ribozyme acts on another => acts on another => … until a cycle forms + the cycle results in the replication of the actors in the cycle
- Could the RNA world have been preceded by some other genetic system?
- RNA world to a DNA-protein world?
Discussion questions
- Alternatives to the RNA world hypothesis?
- Lipid World Hypothesis
- ‘compartment first’ hypothesis
- Early amphiphile molecules such as lipids or fatty acids would have spontaneously self-assembled into liposomes, which are simple vesicles akin to soap bubbles (Banzhaf and Yamamoto, 2015)
- Metabolism-first hypothesis
- Life bootstrapped from a web of chemical reactions forming a primitive metabolism able to use entergy to maintain itself (Banzhaf and Yamamoto, 2015)
- Lipid World Hypothesis
- What is the role of digital systems in origins of life/RNA world research?
- Simulated chemistry systems (e.g., modeling actual chemical reactions) <========> ALife artificial chemistry systems
More resources
- YouTube video introducing the RNA World hypothesis by Stated Clearly
- Banzhaf, W., & Yamamoto, L. (2015). Artificial chemistries. MIT Press.
- Can usually be found in the BEACON graduate student exhibit (on one of the bookshelves).
- Unlike most captive animal exhibits, you are welcome to place food into the enclosure!
- See chapter 6 (section 6.2)
- Can usually be found in the BEACON graduate student exhibit (on one of the bookshelves).
- Black, R. A., Blosser, M. C., Stottrup, B. L., Tavakley, R., Deamer, D. W., & Keller, S. L. (2013). Nucleobases bind to and stabilize aggregates of a prebiotic amphiphile, providing a viable mechanism for the emergence of protocells. Proceedings of the National Academy of Sciences, 110(33), 13272–13276. https://doi.org/10.1073/pnas.1300963110
- Cool work investigating how primordial cells that combined RNA (which functioned as catalysts and carriers of genetic material) and an encapsulating membrane might have come about.
May 31 - Population-based Simulation of Gender Inequality Issues (Matthew Andres Moreno)
Paper: Bullinaria, J. A. (2016). Population-based Simulation of Gender Inequality Issues. Proceedings of the Artificial Life Conference 2016, 452–459. https://doi.org/10.7551/978-0-262-33936-0-ch073 .
Discussion Topics
- Methodology
- Why use agent-based models instead of differential equations?
- Weak cited/empirical support for parameter settings/assumptions
-
The baseline simulations suggest that a promotion fraction of 0.06, a 4 years wait for eligibility, and giving up after twelve years, provides a reasonably realistic basis for the forthcoming simulations.
-
So far, the simulations have been run for many generations to allow enough time for the various population distributions to stabilize,
-
In some species, such factors may be encoded genetically, but for current human professions it is more likely that such information will be passed on mimeticaly, in the form of social learning or mimicry (Bullinaria, 2010).
-
- Figures
- labels
- bitmap versus vector
- error bars (what do they represent?)
- making use of line style in addition to color
- so many error bars it looks like a smear
- Language makes it unclear whether or not certain work was done
-
Discrimination or intervention in that process are other key factors to be explored.
-
It is also possible that varying percentages of individuals leave the working population for other reasons. Such details will need to be explored.
-
For situations that have learning or experience increase the individuals’ abilities in line with the number of yeawrs in their chosen profession, or at each stage in that professeion, it will be interesting to investigate the different age distributions that emerge for each gender at each stage, and to go on to explore the effect of factors such as maternity leave.
-
- Unusually verbose/defensive
-
However, those cases were still run to provide a check that no unexpected biases exist in the simulations.
-
It is inevitable that some readers will disagree with the particular assumptions and simplifications employed in the simulations presented here. Hopefully progress can be made by other researchers using the approach to test the consequences of varying those assumptions and simplifications, and performing simulations more carefully matched to their own data and beliefs.
-
- Didn’t put the one applicable tidbit in the conclusion (although mentioned elsewhere): to differentiate between descrimination and innate ability difference, look for relatively greater ability in the minority gender members at higher eschelons of the hierarchy
- conclusion should tell the broader impact/applications of the research
June 7 - Austin Ferguson
- Compeau, P. (2019). Establishing a computational biology flipped classroom. PLOS Computational Biology, 15(5), e1006764. https://doi.org/10.1371/journal.pcbi.1006764
Points of Note
- Academics are often examples of survivor bias in the education system.
- Most academics can handle a lecture, even if it is not the most effective for them.
- Bloom’s Taxonomic Pyramid
- “Flipped Classrooms”
- Briefly, students handle the basics of understanding on their own outside of class.
- Opens class time up for potentially more engaging activities.
- Bishop and Verleger - Only truly flipped if fully automated. (i.e., not just reading or watching videos)
- MOOC - Massive Open Online Course & MAIT - Massive Adaptive Interactive Text
- Author’s experience with a flipped classroom
- Spring 2014 - ~70 students used MAIT and wrote short progress reports, in-person discussions were guided Q&A
- Spring 2016 - Six students, in-person sessions were switched to peer-to-peer discussion
- Spring 2017 - 30 students, split evenly into four groups? Classes featured a short, tangential lecture, some peer Q&A, and guided group discussion.
- Spring 2018 - Larger cohort but with 4-5 student breakouts doing discussion questions, challenging problems, and guided write-ups.
- Issues, as identified by the author
-
- Motivating students, particularly those with little interest in the subject, can be dificult with the demand of a flipped class. The author also notes a bimodality of students either loving or hating the structure.
-
- Cohort size can play a significant role in success, and there are few resources to help.
-
- It can be dificult to convince students of the classroom shift. The author suggests a “sales pitch” at the semester start to convince them of the flaws of lecturing.
-
- The instructor may have to sacrifice breadth for depth when it comes to student understanding of course content.
-
- When creating a flipped classroom, do you decide on in-class plans first instead of designing in-class activities around available online resources?
- Active learning may be responsible for some extent of this success of flipped classrooms?
- How much?
Discussion Prompts
- Those of you who have experience with different teaching styles, can you elaborate? Weigh the pros and cons, and maybe what could have been better?
- This can be as an instructor or a student!
- What other (hopefully somewhat successful) pedagogical methods exist that I probably haven’t heard of?
- Pedagogical papers are much different than what we normally read.
- Will this always be the case? Any foresight here?
- Tips for finding appropriate articles for someone new to teaching?
- Anything else related to teaching / teaching styles!
- How much?
June 14 - BEACON Seminar (Mark Reimers)
June 21 - Josh Nahum
Paper: Louis P. Elliott and Barry W. Brook (2007). Revisiting Chamberlin: Multiple Working Hypotheses for the 21st Century. BioScience, Volume 57, Issue 7, July 2007, Pages 608–614, https://doi.org/10.1641/B570708.
Optional extra reading:
Paper: T. C. Chamberlin (1965). The Method of Multiple Working Hypotheses. Science New Series, Vol. 148, No. 3671 (May 7, 1965), pp. 754-759.