The purpose of this forum is to introduce notable papers and books published by you and other persons. The work can be new or old, but it should be of wide interest and high quality. A brief comment on the significance of the work should be attached. The current categories of the subjects are (1) adaptation, (2) behavioral evolution, (3) dosage compensation, (4) evo-devo, (5) gene evolution, (6) genomic evolution, (7) molecular phylogeny, (8) natural selection, (9) phenotypic evolution, (10) sensory receptors, (11) sex chromosomes, (12) sex determination, (13) speciation, (14) symbiosis and evolution, and (15) horizontal gene transfer. However, new categories can be added if necessary. Emphasis will be given on the biological work rather than on the mathematical. Any person may post a paper by sending it to one of the editors listed below. We also welcome your comments on posted work, but we moderate all the comments to control spam. This forum is primarily for scientific discussion and to construct a database for good molecular evolution papers.

Wednesday, February 27, 2013

ENCODE - All about "Functions"

Contributed by: Jianzhi Zhang

In 2012, the 288-million-dollar ENCyclopedia Of DNA Elements (ENCODE) project concluded in its 442-author Nature article that 80% of the human genome are functional. The completion of this massive study was regarded by both Nature and Science as one of the most important scientific accomplishments of the year. But are these 442 scientists correct?
Dan Graur and five colleagues have now analyzed the ENCODE paper. Their conclusion is shocking, to say the least. They found that the ENCODE conclusion was erroneous and was reached mainly “(1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect”. The number and seriousness of the errors and inconsistencies they identified from the ENCODE paper are horrifying. One cannot help but wonder where the reviewers of the ENCODE project/paper were and what the 288 million dollars would accomplish if used to fund 200 NIH R01 grants.
I recommend Graur et al.’s paper to all biologists, evolutionary or not, because it deals with some of the most fundamental concepts in biology with unusual clarity and wit. It also prompts one to ponder on the pros and cons of big science vs. small science. Last but not least, if you are intelligent, you will enjoy reading this 43-page PDF.

The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74. 
Graur, D., Zheng, Y., Price, N., Azevedo, R. B. R., Zufall1 R. A., and Elhaik E. 2013. On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol. Evol., published February 20, 2013, doi:10.1093/gbe/evt028