We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate (...) assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments. 10.1126/science.1151721. (shrink)

The aim of this article is to discuss the idea that the notion of topos could become the future mathematics of AI, by giving more emphasis to geometric forms, compared to the currently mainstream approach, which favors numbers through statistical procedures. AI engineers are looking for theories that can formalize the basic elements that shape their daily work, as well as the basic operations that structure how the human brain works. The notion of topos could contribute largely to satisfying these (...) two main aspirations of AI engineering. The article is a part of a questioning on the nature of intelligence and supposedly intelligent machines. In this respect, it would be useful to enrich the approach that assimilates the topos as a kind of bridge that removes all the inessential aspects of things to be connected to keep an common essence that associates mathematical things. One of the most promising avenues from the archeology of the discourse on the topos is the reading by meaning. This art of reading well gives rise to the notion of conceptual strata which shows that the things to be connected have a layered configuration. What seems insignificant –in view of a supposed essence– through one conceptual stratum, might seem important through another, even capital. Rather than calling something ‘insignificant’, a consistent relativism of ‘insignificant for’ would be more appropriate, according to the conceptual stratum considered. (shrink)