Genome Sizes and the Benford Distribution

BACKGROUND: Data on the number of Open Reading Frames (ORFs) coded by genomes from the 3 domains of Life show the presence of some notable general features. These include essential differences between the Prokaryotes and Eukaryotes, with the number of ORFs growing linearly with total genome size for the former, but only logarithmically for the latter. RESULTS: Simply by assuming that the (protein) coding and non-coding fractions of the genome must have different dynamics and that the non-coding fraction must be particularly versatile and therefore be controlled by a variety of (unspecified) probability distribution functions (pdf's), we are able to predict that the number of ORFs for Eukaryotes follows a Benford distribution and must therefore have a specific logarithmic form. Using the data for the 1000+ genomes available to us in early 2010, we find that the Benford distribution provides excellent fits to the data over several orders of magnitude. CONCLUSIONS: In its linear regime the Benford distribution produces excellent fits to the Prokaryote data, while the full non-linear form of the distribution similarly provides an excellent fit to the Eukaryote data. Furthermore, in their region of overlap the salient features are statistically congruent. This allows us to interpret the difference between Prokaryotes and Eukaryotes as the manifestation of the increased demand in the biological functions required for the larger Eukaryotes, to estimate some minimal genome sizes, and to predict a maximal Prokaryote genome size on the order of 8-12 megabasepairs. These results naturally allow a mathematical interpretation in terms of maximal entropy and, therefore, most efficient information transmission

HYBRIDGEN: A MODEL FOR THE STUDY OF QCD HYBRID STATES.

We study the mixing of excited states of a Hydrogen atom in a cavity with de-excited states plus a confined photon as a model for the coupling of quark-antiquark and quark-antiquark-gluon hybrid states in QCD. For an interesting range of parameters, the results are analytic. We find a case for which wavefunctions (and hence decay patterns) may be at odds with mass with respect to identification of a state as hybrid or not

The Number of ORFs in Each Genome vs. Genome Size for the Three Extant Domains of Life on Earth.

<p>The points are data from 1128 genomes available on the GOLD database <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036624#pone.0036624-The1" target="_blank">[3]</a> in early 2010. In this log-log plot, the <i>x</i>-axis represents the genome size (<i>G</i>) in kilobasepairs. For each genome we plot on the <i>y</i>-axis the number of ORFs quoted for the genome in the above database. In order to facilitate comparisons, we have drawn a red diagonal line on a vertical/horizontal scale where 1 vertical axis unit corresponds to 1 kbp on the horizontal axis. The Prokaryotic genomes cluster around this (slope = 1) line. The fit to the Prokaryotes given by Eqn. (6) is represented here as a cyan line. The dashed line represents the best fit to the Eukaryotic ORFs and corresponds to a Benford distribution, Eqn. (11), if we neglect the statistically insignificant contribution from the combination of the first two terms, . Note the wide range of genome sizes that the fit accommodates. See the Discussion Section regarding the right-hand axis.</p