Deadline for Outline: October 4th (or before)

The outline should include the overall structure of the essay (e.g., introduction, thesis, antithesis, synthesis, conclusion) AND a collection of the ideas that you plan to cover in the different parts.

Deadline for the 1st Draft: October 25th (or before - If you submit early, you may get my comments back before Thanksgiving)

Deadline for final version: December 6th (or before)

Possible Topics:

What are the units of natural selection?

Genes, Organisms, Communities - One interesting angle might be to push this to the extremes: individual nucleotides can hardly be considered units of selection, nor the can the biosphere as a whole be considered as possible units of selection, at least is selection is defined as survival of the fittest (see Inkpen and Doolittle's papers on the "Its the song not the singer" seletion here and here).

Can the genome be considered as an ecosystem?

Our genome consists to a large (or very large) part out of former selfish genetic elements that propagated and some still propagate in our genome. What, if any. is missed in this gene centered view of the genome?

Can ecological concepts be applied to relations between genes?

Symbiosis (= mutualism, parasitism, or commensalism) are usually applied to relations between organisms. However, molecular parasites, selfish genetic elements, and even protein domains can have (or "might have" or "always have") relationships to one another that might be described using the same terminology.

Trash to treasure - treasure to trash

Discuss one or more examples of selfish genetic elements and molecular parasites (more vermin than trash) that over time evolved to make positive contributions to the host's fitness (possible are inteins, introns, nonsense-mediated mRNA decay pathway, hedgehog proteins).
Include a brief discussion whether or not this contribution initially qualifies as a nearly neutral pathway towards higher complexity.

Items to think about:

• Selfishness, parasitism and altruistic cooperation within the human genome.
• Can ecological terms be used to describe interactions at the gene and genome level?
• To what extent can/need genes be considered as the unit for selection?
• How do species become more fit?
• Is evolution driven by selfishness and competition (nature red in tooth and claw), or by cooperation (symbiosis, lichen, kefir endosymbionts)
• Frequently competition for resources acting at a level of subunits is counterproductive: e.g., selfish cells in a metazoan turn into cancer, in social insects there is no or little competition between members of the same state (and frequently they are genetically identical). Can/could this be different at the gene level?
• Should there be a distinction between selfish and parasitic genes? Altruism can be a form of selfishness (I help you, you help me, life is not a zero sum game). According to Richard Dawkins' original definition all genes are selfish, even the ones cooperating with each other.

Suggested reading:

• Discussion of the encode project by W. Ford Doolittle and Dan Graur (a more recent article from Dan on the maximally functional part of the human genome is here)
• Wikipedia on Group selection and Units of selection
  
• Eugene V. Koonin: Evolution of genome architecture
  
• John C. Avise: Evolving Genomic Metaphors: A New Look at the Language of DNA
• Steven J. Gould: Gulliver's further travels: the necessity and difficulty of a hierarchical theory of selection.
  
• Koschwanez JH, Foster KR, Murray AW (2011) Sucrose Utilization in Budding Yeast as a Model for the Origin of Undifferentiated Multicellularity. PLoS Biol 9(8): e1001122 (cheating, cooperation and the rise of multicellularity in yeast)
  
• Robert Axelrod; William D. Hamilton: The Evolution of Cooperation or here Science, New Series, Vol. 211, No. 4489. (Mar. 27, 1981), pp. 1390-1396.
  
• Connie Barlow, "From Gaia to Selfish Genes", pp. 195 - 213 and 238-239 (available at WebCT's reading materials or via Google books)
• Sorin Sonea: The global organism: A new view of bacteria. The Sciences 1988 (On HuskyCT or retrieve through Google scholar - UConn Law has a subscription)
• Paul B. Rainey: Essay on "Unity from conflict" Nature 446, 616 (5 April 2007) | doi:10.1038/446616a; Published online 4 April 2007
  
• Richard Dawkins: The selfish gene. Oxford University Press; 1976.
• Eugene V. Koonin: Viruses and mobile elements as drivers of evolutionary transitions, Philos Trans R Soc Lond B Biol Sci. 2016 Aug 19;371(1701). pii: 20150442. doi: 10.1098/rstb.2015.0442.