Long-Term Memory: Scaling of Information to Brain Size

The material bases of information - paper, computer discs - usually scale with information quantity. Large quantities of information usually require large material bases. Conventional wisdom has it that human long-term memory locates within brain tissue, and so might be expected to scale with brain size which, in turn, depends on cranial capacity. Large memories, as in savants, should always require large heads. Small heads should always scale with small memories. While it was previously concluded that neither of these predictions was invariably true, the evidence was weak. Brain size also depends on ventricle size, which can remain large in some survivors of childhood hydrocephaly, occupying 95% of cranial volume. Yet some of these have normal or advanced intelligence, indicating little impairment of long-term memory. This paradox challenges the scaling hypothesis. Perhaps we should be looking further afield?Comment: 10 pages, 1 figure; submitted to Biological Theory 20th Feb 2013; a requested revision was submitted 28th July 201

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignment

Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition is still an unsolved puzzle. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular electrostatic ones. In this proposed mechanism, sequences having the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts; the difference termed the recognition energy. Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding was termed the recognition well. We find that there is recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations, and consider more rigorously the optimization of the orientations of the fragments about their long axes. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. However when torsional flexibility of the DNA molecules is introduced, we find excellent agreement between analytical approximation and simulation.Comment: Paper with supplemental material attached. 41 pages in all, 4 figures in main text, 3 figures in supplmental. To be submitted to Journa