The Ontological Basis of Strong Artificial Life

This article concerns the claim that it is possible to create living organisms, not merely models that represent organisms, simply by programming computers ("virtual" strong alife). I ask what sort of things these computer-generated organisms are supposed to be (where are they, and what are they made of?). I consider four possible answers to this question: (a) The organisms are abstract complexes of pure information; (b) they are material objects made of bits of computer hardware; (c) they are physical processes going on inside the computer; and (d) they are denizens of an entire artificial world, different from our own, that the programmer creates. I argue that (a) could not be right, that (c) collapses into (b), and that (d) would make strong alife either absurd or uninteresting. Thus, "virtual" strong alife amounts to the claim that, by programming a computer, one can literally bring bits of its hardware to life

Geant4 Applications for Modeling Molecular Transport in Complex Vacuum Geometries

We discuss a novel use of the Geant4 simulation toolkit to model molecular transport in a vacuum environment, in the molecular flow regime. The Geant4 toolkit was originally developed by the high energy physics community to simulate the interactions of elementary particles within complex detector systems. Here its capabilities are utilized to model molecular vacuum transport in geometries where other techniques are impractical. The techniques are verified with an application representing a simple vacuum geometry that has been studied previously both analytically and by basic Monte Carlo simulation. We discuss the use of an application with a very complicated geometry, that of the Large Synoptic Survey Telescope camera cryostat, to determine probabilities of transport of contaminant molecules to optical surfaces where control of contamination is crucial.Comment: 7 pages, 4 figures, 2 tables, to appear in IJMSSC, updated to accepted versio

Why does low intensity, long-day lighting promote growth in Petunia, Impatiens, and tomato?

Numerous reports demonstrate that low intensity, long-day (LD) lighting treatments can promote growth. However, there are conflicting suggestions as to the mechanisms involved. This study examines the responses of Petunia, Impatiens, and tomato to LD lighting treatments and concludes that no single mechanism can explain the growth promotion observed in each case. Petunia showed the most dramatic response to photoperiod; up to a doubling in dry weight (DW) as a result of increasing daylength from 8 h d–1 to 16 h d–1.This could be explained by an increase in specific leaf area (SLA) comparable to that seen with shading. At low photosynthetic photon flux densities (PPFD), the increased leaf area more than compensated for any loss in photosynthetic capacity per unit leaf area. In Petunia, the response may, in part, have also been due to changes in growth habit. Impatiens and tomato showed less dramatic increases in DW as a result of LD lighting, but no consistent effects on SLA or growth habit were observed. In tomato, increased growth was accompanied by increased chlorophyll content, but this had no significant effect on photosynthesis. In both species, increased growth may have been due to a direct effect of LD lighting on photosynthesis. This is contrary to the generally held view that light of approx. 3 – 4 μmol m–2 s–1 is unlikely to have any significant impact on net photosynthesis. Nevertheless, we show that the relationship between PPFD and net photosynthesis is non-linear at low light levels, and therefore low intensity LD lighting can offset respiration very efficiently. Furthermore, a small increase in photosynthesis will have a greater impact when ambient light levels are low

Localization of the Functional Domains of Human Tissue Inhibitor of Metalloproteinases-3 and the Effects of a Sorsby's Fundus Dystrophy Mutation

A transient COS-7 cell expression system was used to investigate the functional domain arrangement of tissue inhibitor of metalloproteinases-3 (TIMP-3), specifically to assess the contribution of the amino- and carboxylterminal domains of the molecule to its matrix metalloproteinase (MMP) inhibitory and extracellular matrix (ECM) binding properties. Wild type TIMP-3 was entirely localized to the ECM in both its glycosylated (27 kDa) and unglycosylated (24 kDa) forms. A COOH-terminally truncated TIMP-3 molecule was found to be a non- ECM bound MMP inhibitor, whereas a chimeric TIMP molecule, consisting of the NH2-terminal domain of TIMP-2 fused to the COOH-terminal domain of TIMP-3, displayed ECM binding, albeit with a lower affinity than the wild type TIMP-3 molecule. Thus the functional domain arrangement of TIMP-3 is analogous to that seen in TIMP-1 and -2, namely that the NH2-terminal domain is responsible for MMP inhibition whereas the COOH-terminal domain is most important in mediating the specific functions of the molecule. A mutant TIMP-3 in which serine 181 was changed to a cysteine, found in Sorsby’s fundus dystrophy, a hereditary macular degenerative disease, was also expressed in COS-7 cells. This gave rise to an additional 48-kDa species (possibly a TIMP-3 dimer) that retained its ability to inhibit MMPs and localize to the ECM. These data favor the hypothesis that the TIMP-3 mutations seen in Sorsby’s fundus dystrophy contribute to disease progression by accumulation of mutant protein rather than by the loss of functional TIMP-3

Measuring Complexity in an Aquatic Ecosystem

We apply formal measures of emergence, self-organization, homeostasis, autopoiesis and complexity to an aquatic ecosystem; in particular to the physiochemical component of an Arctic lake. These measures are based on information theory. Variables with an homogeneous distribution have higher values of emergence, while variables with a more heterogeneous distribution have a higher self-organization. Variables with a high complexity reflect a balance between change (emergence) and regularity/order (self-organization). In addition, homeostasis values coincide with the variation of the winter and summer seasons. Autopoiesis values show a higher degree of independence of biological components over their environment. Our approach shows how the ecological dynamics can be described in terms of information.Comment: 6 pages, to be published in Proceedings of the CCBCOL 2013, 2nd Colombian Computational Biology Congress, Springe

A novel tissue inhibitor of metalloproteinases-3 mutation reveals a common molecular phenotype in sorsby's fundus dystrophy

Sorsby’s fundus dystrophy (SFD) is a dominantly inherited degenerative disease of the retina that leads to loss of vision in middle age. It has been shown to be caused by mutations in the gene for tissue inhibitor of metalloproteinases-3 (TIMP-3). Five different mutations have previously been identified, all introducing an extra cysteine residue into exon 5 (which forms part of the C-terminal domain) of the TIMP-3 molecule; however, the significance of these mutations to the disease phenotype was unknown. In this report, we describe the expression of several of these mutated genes, together with a previously unreported novel TIMP-3 mutation from a family with SFD that results in truncation of most of the C-terminal domain of the molecule. Despite these differences, all of these molecules are expressed and exhibit characteristics of the normal protein, including inhibition of metalloproteinases and binding to the extracellular matrix. However, unlike wild-type TIMP-3, they all form dimers. These observations, together with the recent finding that expression of TIMP-3 is increased, rather than decreased, in eyes from patients with SFD, provides compelling evidence that dimerized TIMP-3 plays an active role in the disease process by accumulating in the eye. Increased expression of TIMP-3 is also observed in other degenerative retinal diseases, including the more severe forms of agerelated macular degeneration, the most common cause of blindness in the elderly in developed countries. We hypothesize that overexpression of TIMP-3 may prove to be a critical step in the progression of a variety of degenerative retinopathies

Australian Indigenous knowledge and libraries

The library and information profession has much to learn to meet the information needs of Indigenous people and appropriately manage Indigenous knowledge within their organisations. The Indigenous perspective can well understand the profession\u27s desire to have clear prescriptions for practice and practical assistance. However, the path to developing clear and high standards of practice in this area rests on building a strong foundation for understanding what informs the concerns of Indigenous people about the intersection of their knowledge and cultural materials with library and archival systems and practice