Can't Live Without 'Em: The Logic and Implications of "Essential" Genes
In a classic scene near the end of Jules Verne's Around The World in 80 Days, Phileas Fogg buys the Henrietta, the steamship on which he is racing across the Atlantic. His first order as new owner is to tell the captain, "Have the interior seats, frames, and bunks pulled down, and burn them" -- all this to maintain pressure in the ship's boiler. Over the next two days, everything else nonessential and flammable on the Henrietta is fed into the boiler, until the ship is "only a flat hulk." But a hulk that nevertheless would still carry Fogg to his destination in England.
The question of what parts in any complex system are essential for its key functions, or indeed its very existence, is one of the most interesting puzzles in engineering and biology. A new open-access paper, "The essential genome of a bacterium," describes the most refined technique yet employed -- down to "a resolution of a few base pairs" -- to map those genes required by a bacterial cell for its existence. Using Caulobacter crescentus, an alpha-proteobacterium commonly found in lakes and streams, a team at Stanford generated (via transposon mutagenesis) 428,735 disruptive insertions in the 4 million base pair genome of the species.
"There were many surprises in the analysis of the essential regions of Caulobacter's genome," said Lucy Shapiro, PhD, the paper's senior author. "For instance, we found 91 essential DNA segments where we have no idea what they do. These may provide clues to lead us to new and completely unknown bacterial functions."The study concluded that slightly more than 12 percent of Caulobacter's genome was essential, comprising 1012 features: 480 ORFs (protein-coding open reading frames), 402 regulatory sequences and 130 non-coding elements, including the mysterious sequences of unknown function mentioned by Shapiro.
If you want to tease out some of the implications of this experiment for intelligent design, take a look at this paper. While the authors are writing within an explicitly Darwinian framework, searching for the foundations of what they call "synthetic biology," they acknowledge that "top-down" (i.e., subtractive) analyses (the new Stanford Caulobacter experiment is an excellent example of such) have revealed that the essential functions of cells possess a breathtaking complexity of unanticipated subtlety and interconnectedness. "In other words," they write, "the closer to life creation we are, the most intricate [life] appears to be" (p. 7).
Here's another potential design implication. Click on this link, and scroll down to the bottom of the figure (4C). Notice that Caulobacter and E. coli have very significant numbers of species-specific (i.e., taxonomically unique) essential ORFs (129 unique to Caulobacter, and 235 unique to E. coli, respectively). Is it possible to transform the essential parts of these two groups (within the phylum Proteobacteria), from a common ancestor, via an undirected process?