A grounded theory of abstraction in artificial intelligence

In artificial intelligence, abstraction is commonly used to account for the use of various levels of details in a given representation language or the ability to change from one level to another while preserving useful properties. Abstraction has been mainly studied in problem solving, theorem proving, knowledge representation (in particular for spatial and temporal reasoning) and machine learning. In such contexts, abstraction is defined as a mapping between formalisms that reduces the computational complexity of the task at stake. By analysing the notion of abstraction from an information quantity point of view, we pinpoint the differences and the complementary role of reformulation and abstraction in any representation change. We contribute to extending the existing semantic theories of abstraction to be grounded on perception, where the notion of information quantity is easier to characterize formally. In the author's view, abstraction is best represented using abstraction operators, as they provide semantics for classifying different abstractions and support the automation of representation changes. The usefulness of a grounded theory of abstraction in the cartography domain is illustrated. Finally, the importance of explicitly representing abstraction for designing more autonomous and adaptive systems is discussed.     

An Evaluation of the Non-Neutrality of Money

This paper evaluates the effect of a change in the quantity of money on relative prices in the U.S. economy based on quarterly time-series for the period of 1959 to 2013. We also estimate the implication of a change in relative prices on the rate of inflation and macroeconomic variables. The empirical results indicate that the change of money supply not only affects relative prices but also affects the inflation rate and real variables, such as investment, natural rate of unemployment and potential GDP, through the change in relative prices. The relevant finding of our study is that money is not neutral in a non-traditional sense because a change in the money supply disturbs relative prices and, consequently, the allocation of resources in the economy. This finding has serious implications that must be considered in the transmission mechanisms of monetary policy.     

Can lemurs (<Emphasis Type="Italic">Eulemur fulvus</Emphasis> and <Emphasis Type="Italic">E. macaco</Emphasis>) use abstract representations of quantities to master the reverse-reward contingency task?

In previous studies we demonstrated that brown and black lemurs (Eulemur fulvus and E. macaco) showed self-control abilities under a reverse-reward contingency. They were able to significantly select the smaller quantity of food to be rewarded with the larger one and to generalize this ability when presented with two rewards that differed in quality. In the present study, previously trained subjects had to choose between graphic representations of two different quantities of food under the reverse-reward contingency. Three out of four subjects learned to associate a graphic representation of the reward with the corresponding quantity. Only one subject consistently selected the representation of the smaller quantity to be rewarded with the larger quantity of food and therefore showed abstraction as well as relative numerousness skills. Indeed, she was able to discriminate between representations of different quantities and to ordinate them. We discuss how primates mentally represent food quantities and how self-control is involved in foraging strategies.     

An algorithm for comparing multiple RNA secondary structures

A new distributed computational procedure is presented for rapidlydetermining the similarity of multiple conformations of RNAsecondary structures. A data abstraction scheme is utilizedto reduce the quantity of data that must be handled to determinethe degree of similarity among multiple structures. The methodhas been used to compare 200 structures with easy visualizationof both those structures and substructures that are similarand those that are vastly different. It has the capability ofprocessing many more conformations as a function of researchrequirements. The algorithm is described as well as some suggestionsfor future uses and extensions. Received on October 29, 1987; accepted on May 4, 1988     

Trust and Reciprocity: Are Effort and Money Equivalent?

Trust and reciprocity facilitate cooperation and are relevant to virtually all human interactions. They are typically studied using trust games: one subject gives (entrusts) money to another subject, which may return some of the proceeds (reciprocate). Currently, however, it is unclear whether trust and reciprocity in monetary transactions are similar in other settings, such as physical effort. Trust and reciprocity of physical effort are important as many everyday decisions imply an exchange of physical effort, and such exchange is central to labor relations. Here we studied a trust game based on physical effort and compared the results with those of a computationally equivalent monetary trust game. We found no significant difference between effort and money conditions in both the amount trusted and the quantity reciprocated. Moreover, there is a high positive correlation in subjects' behavior across conditions. This suggests that trust and reciprocity may be character traits: subjects that are trustful/trustworthy in monetary settings behave similarly during exchanges of physical effort. Our results validate the use of trust games to study exchanges in physical effort and to characterize inter-subject differences in trust and reciprocity, and also suggest a new behavioral paradigm to study these differences.     

Automated and dynamic abstraction of MPI application performance

Developing an efficient parallel application is not an easy task, and achieving a good performance requires a thorough understanding of the program’s behavior. Careful performance analysis and optimization are crucial. To help developers or users of these applications to analyze the program’s behavior, it is necessary to provide them with an abstraction of the application performance. In this paper, we propose a dynamic performance abstraction technique, which enables the automated discovery of causal execution paths, composed of communication and computational activities, in MPI parallel programs. This approach enables autonomous and low-overhead execution monitoring that generates performance knowledge about application behavior for the purpose of online performance diagnosis. Our performance abstraction technique reflects an application behavior and is made up of elements correlated with high-level program structures, such as loops and communication operations. Moreover, it characterizes all elements with statistical execution profiles. We have evaluated our approach on a variety of scientific parallel applications. In all scenarios, our online performance abstraction technique proved effective for low-overhead capturing of the program’s behavior and facilitated performance understanding.     

Mechanism-based inhibitors of dopamine beta-hydroxylase

The copper-containing monooxygenase dopamine beta-hydroxylase catalyzes the hydroxylation of dopamine at the benzylic position to form norepinephrine. Mechanism-based inhibitors for dopamine beta-hydroxylase have been used as probes of the mechanism of catalysis. The variety of such inhibitors that have been developed for this enzyme can be divided into three groups: (i) those in which the inactivating species is formed by abstraction of a hydrogen atom to form a radical intermediate; (ii) those in which the inactivating species is formed by abstraction of an electron to form an epoxide-like intermediate; and (iii) those in which the product is the inactivating species. A mechanism consistent with inactivation by all three groups of inhibitors which proposes that hydroxylation of dopamine by dopamine beta-hydroxylase involves formation of a benzylic radical has been developed. The benzylic radical is formed by abstraction of a hydrogen atom from the substrate by a high-potential copper-oxygen species.     

Ethnographic Critique and Technoscientific Narratives: The Old Mole, Ethical Plateaux, and the Governance of Emergent Biosocial Polities

A reading of the puzzle novel ViennaBlood, by Adrian Mathews, is juxtaposed tothree ethnographic sketches of contemporaryethical plateaus or domains of ethicalchallenge – the challenges of informed publicconsent to new technologies, the seductions todo whatever is medically possible (sometimes atthe expense of quality of life or the `gooddeath'), and the power of money in driving thebiotechnological industries. ViennaBlood deals with precautionary germplasmmodification and chemical camouflage justifiedas protection against ethnically-targetedbiological warfare, and touches on a series oftechnologies such as new reproductivetechnologies, genetic engineering, andcryptographic attacks and defenses, as well asthe ability to evade regulatory controls. Suchtechnoscientifically informed novels are usefulas cautionary tales, in exploring thecomplexity and interaction among newtechnologies, and the phantasmagoria that helpdrive new technologies. They are not so good atthinking through institutional development: achallenge for ethnography and new socialtheory. Ethnography, like novels, can functionas checks on the mechanisms of abstraction anduniversalization that frequently bedevil thenon-anthropological, non-cross-culturally orcross-temporally comparative, social sciences.Questions are raised about new or emergentbiosocialities, forms of governance, and formsof cultural critique.     

Discounting of delayed hypothetical money and food: effects of amount

Delay discounting research determines how the value of an outcome is affected by delay to its receipt. Research so far shows that consumable outcomes are discounted more steeply by delay than money. Prior studies, however, have used large amounts of the outcomes (e.g. 100 dollars worth) that would not typically be consumed in one bout, unlike the corresponding amount of money (e.g. 100 dollars ). This experiment examined whether small amounts of food would be discounted more steeply than money, as occurs with larger amounts. One hundred and two adults indicated their preferences in a series of choices for two hypothetical outcome types: immediate versus delayed food and immediate versus delayed money. Participants made choices involving either relatively small maximum amounts of food (10 dollars worth) and money (10 dollars) or for relatively large maximum amounts of food (100 dollars worth) and money (100 dollars ). In the within-subject comparisons, food was discounted more steeply by delay than money for both groups. In the between-subject comparisons, different amounts of the commodities were affected similarly by delay. Overall, these results suggest that steeper discounting of consumable outcomes than money is a fairly robust phenomenon, occurring with relatively small amounts of outcomes as well as with larger amounts.     

How to manifest abundance: money and the rematerialization of exchange in Sedona,Arizona, USA

Manifestation is a spiritual practice with material gains. It is a way for those involved with spirituality in Sedona, Arizona, to make money as required while maintaining a level of consonance between their economic life and spiritual path. Analysing the entwinement of economics and religion in everyday life, this article contributes to literature on spiritual economies and, more broadly, to the anthropology of money. Manifestation is a way of figuratively rematerializing exchange, mirrored in preferences for trade and barter and currency backed by gold. Dematerialized money – the stocks, bonds, and derivatives of high finance – is rejected as enacting a low vibration; it is negatively valenced in cosmologies of spirituality. Preferences for money forms reveal responses and reactions to neoliberal capitalism in an embedded, industrialized economy.     

Improved hybrid optimization algorithm for 3D protein structure prediction

Diuron, a chlorine-substituted dimethyl herbicide, is widely used in agriculture. Though the degradation of diuron in water has been studied much with experiments, little is known about the detailed degradation mechanism from the molecular level. In this work, the degradation mechanisms for OH-induced reactions of diuron in water phase are investigated at the MPWB1K/6–311+G(3df,2p)//MPWB1K/6–31+G(d,p) level with polarizable continuum model (PCM) calculation. Three reaction types including H-atom abstraction, addition, and substitution are identified. For H-atom abstraction reactions, the calculation results show that the reaction abstracting H atom from the methyl group has the lowest energy barrier; the potential barrier of ortho- H (H1’) abstraction is higher than the meta- H abstraction, and the reason is possibly that part of the potential energy is to overcome the side chain torsion for the H1’ abstraction reaction. For addition pathways, the ortho- site (C (2) atom) is the most favorable site that OH may first attack; the potential barriers for OH additions to the ortho- sites (pathways R7 and R8) and the chloro-substituted para- site (R10) are lower than other sites, indicating the ortho- and para- sites are more favorable to be attacked, matching well with the -NHCO- group as an ortho-para directing group.

‘Bridges to cash’: channelling agency in mobile money

Encountered by mobile money professionals – industry and philanthropic actors seeking to bring mobile phone‐enabled financial products to poor people in the ‘developing world’ – the authors move together with new collaborators to inquire into a problem they had been grappling with for some time. This is the problem of agency; specifically, the agency of ‘mobile money agents’, the people ‘on the ground’ or ‘in the field’ who form a crucial function in permitting others to put cash into an electronic money transfer system and pull cash out of it. These ‘human ATMs’ or ‘bridges to cash’ become the object of analytical scrutiny for mobile money experts and anthropologists. This article takes that analytical scrutiny – and not mobile money agents themselves – as its object. It seeks to understand how ‘agency’ inflects debates over money, its meaning and its pragmatics, and its transformation in new communicative infrastructures, and how it might inform anthropology and political struggles over money and payment.     

Mechanistic diversity in the RuBisCO superfamily: the "enolase" in the methionine salvage pathway in Geobacillus kaustophilus

D-Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme, is the paradigm member of the recently recognized mechanistically diverse RuBisCO superfamily. The RuBisCO reaction is initiated by abstraction of the proton from C3 of the d-ribulose 1,5-bisphosphate substrate by a carbamate oxygen of carboxylated Lys 201 (spinach enzyme). Heterofunctional homologues of RuBisCO found in species of Bacilli catalyze the tautomerization ("enolization") of 2,3-diketo-5-methylthiopentane 1-phosphate (DK-MTP 1-P) in the methionine salvage pathway in which 5-methylthio-d-ribose (MTR) derived from 5'-methylthioadenosine is converted to methionine [Ashida, H., Saito, Y., Kojima, C., Kobayashi, K., Ogasawara, N., and Yokota, A. (2003) A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO, Science 302, 286-290]. The reaction catalyzed by this "enolase" is accomplished by abstraction of a proton from C1 of the DK-MTP 1-P substrate to form the tautomerized product, a conjugated enol. Because the RuBisCO- and "enolase"-catalyzed reactions differ in the regiochemistry of proton abstraction but are expected to share stabilization of an enolate anion intermediate by coordination to an active site Mg2+, we sought to establish structure-function relationships for the "enolase" reaction so that the structural basis for the functional diversity could be established. We determined the stereochemical course of the reaction catalyzed by the "enolases" from Bacillus subtilis and Geobacillus kaustophilus. Using stereospecifically deuterated samples of an alternate substrate derived from d-ribose (5-OH group instead of the 5-methylthio group in MTR) as well as of the natural DK-MTP 1-P substrate, we determined that the "enolase"-catalyzed reaction involves abstraction of the 1-proS proton. We also determined the structure of the activated "enolase" from G. kaustophilus (carboxylated on Lys 173) liganded with Mg2+ and 2,3-diketohexane 1-phosphate, a stable alternate substrate. The stereospecificity of proton abstraction restricts the location of the general base to the N-terminal alpha+beta domain instead of the C-terminal (beta/alpha)8-barrel domain that contains the carboxylated Lys 173. Lys 98 in the N-terminal domain, conserved in all "enolases", is positioned to abstract the 1-proS proton. Consistent with this proposed function, the K98A mutant of the G. kaustophilus "enolase" is unable to catalyze the "enolase" reaction. Thus, we conclude that this functionally divergent member of the RuBisCO superfamily uses the same structural strategy as RuBisCO for stabilizing the enolate anion intermediate, i.e., coordination to an essential Mg2+, but the proton abstraction is catalyzed by a different general base.     

Abstraction and reformulation in artificial intelligence

This paper contributes in two ways to the aims of this special issue on abstraction. The first is to show that there are compelling reasons motivating the use of abstraction in the purely computational realm of artificial intelligence. The second is to contribute to the overall discussion of the nature of abstraction by providing examples of the abstraction processes currently used in artificial intelligence. Although each type of abstraction is specific to a somewhat narrow context, it is hoped that collectively they illustrate the richness and variety of abstraction in its fullest sense.     

Long-range charge transport through double-stranded DNA mediated by manganese or iron porphyrins

Guanine oxidation by electron transfer results in the formation of a guanine radical cation, which is at the origin of long-range charge transport through double-stranded DNA. It is possible to observe guanine lesions at a long distance from the oxidative reagent covalently bound to DNA owing to the migration of the positive hole in the DNA pi-stacks. This phenomenon of long-range hole transport is classically studied in the literature with photosensitizers used as one-electron oxidants. It is shown in the present work that the process of long-range charge transport and the concomitant formation of guanine lesions at a long distance can be observed also in the case of two-electron oxidants. This is the signature of the formation of a transient guanine radical cation in the course of the two-electron abstraction process and consequently evidence of the separated one plus one electron abstraction steps. Long-range charge transport is likely to be a universal mechanism for any two-electron oxidant acting by electron abstraction provided that the second electron abstraction is slower than hole transfer.     

Impact of groundwater abstraction on a Banksia woodland, Swan Coastal Plain, Western Australia

Summary The Gnangara Groundwater Mound, centred 38 km north of Perth, Western Australia, is a large, shallow unconfined aquifer that is currently under abstraction as part of the public metropolitan water supply. To investigate the impact of lowering groundwater levels on a Banksia woodland on the Mound, vegetation monitoring near a groundwater abstraction bore (known as P50) began 1 year before becoming operational. In February 1991, 2 years after abstraction commenced, extensive death of the Banksia overstorey was observed within close proximity of the bore, following a short period of high summer temperatures. The site was subsequently revisited and the understorey floristic composition, abundance and vigour of overstorey species resurveyed, and compared with data collected from a site under long‐term monitoring and not currently influenced by abstraction. A lowering of groundwater level by 2.2 m at P50 between the summers of 1990 and 1991, resulting from the cumulative effects of abstraction and below average annual rainfall (low groundwater recharge), coincided with a loss of between 20 and 80% of adults of overstorey species and up to 64% of adults of understorey species within 200 m of the bore. Over a similar time period no significant decreases in the abundance of overstorey or understorey species were recorded in the monitored site not influenced by groundwater abstraction. Of the overstorey species, Holly‐leaf Banksia (Banksia ilicifolia) displayed the greatest susceptibility and lowest net recovery following the abstraction event at P50. The negative impact of groundwater drawdown on Holly‐leaf Banksia populations makes this overstorey species an important indicator of decreasing groundwater levels on the Gnangara Groundwater Mound. Water stress may have been the primary cause of vegetation death in close proximity to the P50 bore, although this would have been exacerbated by extreme summer temperatures (> 45°C) recorded during February 1991. The P50 scenario represents a localized response to an acute drawdown event, in association with other environmental factors, and provides invaluable information on the assessment of groundwater abstraction and poor groundwater recharge events on a Banksia woodland community. However, there are limitations in using the community response at P50 to manage the impact of drawdown events on other plant communities occurring on sandy, shallow aquifers.     

From philosophy to science (to natural philosophy): evolutionary developmental perspectives

This paper focuses on abstraction as a mode of reasoning that facilitates a productive relationship between philosophy and science. Using examples from evolutionary developmental biology, I argue that there are two areas where abstraction can be relevant to science: reasoning explication and problem clarification. The value of abstraction is characterized in terms of methodology (modeling or data gathering) and epistemology (explanatory evaluation or data interpretation).     

Discounting of delayed hypothetical money, alcohol, and food

For drug-dependent individuals, drugs of abuse that are delayed in time are discounted more steeply than money delayed in time in a hypothetical choice task. The reasons for this finding are not clear. This study examined whether steep discounting of drugs relative to money might be related to the function of drugs as primary/consumable reinforcers and money as a conditioned/non-consumable reinforcer. Twenty adults with no self-reported problems with money, alcohol, or food participated. They indicated their preferences for three hypothetical outcome types: delayed versus immediate money, delayed versus immediate food, and delayed versus immediate alcohol. Both the hyperbolic decay model and area under the curve analysis showed that money was discounted less steeply than alcohol or food, but that alcohol and food were discounted similarly. This finding replicates previous results showing that people without drug abuse problems show steep discounting of alcohol. Furthermore, this finding suggests that alcohol may be steeply discounted as part of a general process involving primary/consumable reinforcers, not necessarily because it is a drug.     

Hydrogen abstraction ability of different aromatic nitroxides

Indolinonic aromatic nitroxides have been shown to efficiently inhibit free radical mediated oxidation reactions in biological systems. Since all antioxidants also possess pro-oxidant activity, possibly through a hydrogen abstraction process from suitable substrates, the relative hydrogen abstraction abilities of these compounds were evaluated. Different hydrogen donors were reacted with an indolinic and two indolinonic nitroxides and the rates of hydrogen abstraction were determined using UV-Vis spectroscopy. From the data obtained, a structure-activity relationship was found. In addition, the hydrogen abstraction ability of these compounds was found to be much greater than that of the aliphatic nitroxide TEMPO, despite existing reports indicating that these two classes of compounds show similar antioxidant activities in biological systems.     

Energetic feasibility of hydrogen abstraction and recombination in coenzyme B(12)-dependent diol dehydratase reaction.

Coenzyme B(12) serves as a cofactor for enzymatic radical reactions. The essential steps in all the coenzyme B(12)-dependent rearrangements are two hydrogen abstraction steps: hydrogen abstraction of the adenosyl radical from substrates, and hydrogen back-abstraction (recombination) of a product-derived radical from 5'-deoxyadenosine. The energetic feasibility of these hydrogen abstraction steps in the diol dehyratase reaction was examined by theoretical calculations with a protein-free, simplified model at the B3LYP/6-311G* level of density functional theory. Activation energies for the hydrogen abstraction and recombination with 1,2-propanediol as substrate are 9.0 and 15.1 kcal/mol, respectively, and essentially not affected by coordination of the substrate and the radical intermediate to K+. Since these energies can be considered to be supplied by the substrate-binding energy, the computational results with this simplified model indicate that the hydrogen abstraction and recombination in the coenzyme B(12)-dependent diol dehydratase reaction are energetically feasible.