Considerations in the aesthetic appeal of scientific papers, 2009:

1. Clear hypothesis and rationale for experiments

2. Conclusions supported by evidence in the paper

3. Figure legends that make the figure clear

4. Transitions from one experiment to the next; rational progression of ideas tested

5. Explanation of why this question is important

6. Discussion of conflicting data if appropriate

7. Diagrams/models to clarify concepts and relationships if appropriate

8. Minimal supplementary figures, none on main points

9. Every Fig/Table in paper actually supports hypothesis, no padding

Nominated Papers Discussed 5/5/09:

Erik Lykken: Celotto and Graveley Alternative splicing of the Drosophila Dscam Pre-mRNA is both temporally and spatially regulated. Genetics 159:599-608 (2001).

Alyssa Ward: Kadonaga and Tjian, Affinity purification of sequence-specific DNA binding proteins. PNAS, USA 83:5889-5893 (1986) Latchman p 195, and Kadonaga et al., Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain, Cell 51:1079-1090 (1987) Latchman p 201. 

Kate Bayliss: Kaffman et al., The receptor Msn5 exports the phosphorylated transcription factor Pho4 out of the nucleus.  Nature 396:482-486 (1998)

Syd Freggiaro: Kwon et al., Nucleosome disruption and enhancement of activator binding by a human SWI/SNF complex.  Nature 370:477-481 (1994)

Amir Nobakht: Cai**, S, Han, H-J, and Kohwi-Shigematsu, T.  Tissue-specific nuclear architecture and gene expression regulated by SATB1.  Nature Genetics 34:42-51 (2003)

Jocelyn Young: Takahashi, K, Tanabe, K, Ohnuki, M, Narita,M, Ichisaka, T, Tomoda, K, and Yamanaka, S. Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors. Cell 131: 1-12 (Nov, 2007)

The vote: Tied between Celotto and Gravely on regulation of splicing of Dscam and Kaffman et al on location control of transcription factor Pho4 by phosphorylation.

Both papers largely fulfilled or exceeded all criteria. Each had one data problem: Kaffman et al showed a gel of phosphorylated and non-phosphorylated Pho4 where they didn’t migrate differently enough to be convincing and Celotto and Gravely had one table concerning differences between D. yakuba and D. melanogaster that was confusing and hard to figure out. In general, both had clear rationales for experiments, were investigating important regulatory phenomena, and wrote clearly about them.