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J D Farmer

Publications and source records attributed to J D Farmer.

At least 19 recordsLinked to original sources
PubMed2004

Basaltic rocks analyzed by the Spirit Rover in Gusev Crater.

The Spirit landing site in Gusev Crater on Mars contains dark, fine-grained, vesicular rocks interpreted as lavas. Pancam and Mini-Thermal Emission Spectrometer (Mini-TES) spectra suggest that all of these rocks are similar but have variable coatings and dust mantles. Magnified images of brushed and abraded rock surfaces show alteration rinds and veins. Rock interiors contain </=25% megacrysts. Chemical analyses of rocks by the Alpha Particle X-ray Spectrometer are consistent with picritic basalts, containing normative olivine, pyroxenes, plagioclase, and accessory FeTi oxides. Mössbauer, Pancam, and Mini-TES spectra confirm the presence of olivine, magnetite, and probably pyroxene. These basalts extend the known range of rock compositions composing the martian crust.

Extraterrestrial Environment↗
PubMed2000

The state and future of Mars polar science and exploration.

As the planet's principal cold traps, the martian polar regions have accumulated extensive mantles of ice and dust that cover individual areas of approximately 10(6) km2 and total as much as 3-4 km thick. From the scarcity of superposed craters on their surface, these layered deposits are thought to be comparatively young--preserving a record of the seasonal and climatic cycling of atmospheric CO2, H2O, and dust over the past approximately 10(5)-10(8) years. For this reason, the martian polar deposits may serve as a Rosetta Stone for understanding the geologic and climatic history of the planet--documenting variations in insolation (due to quasiperiodic oscillations in the planet's obliquity and orbital elements), volatile mass balance, atmospheric composition, dust storm activity, volcanic eruptions, large impacts, catastrophic floods, solar luminosity, supernovae, and perhaps even a record of microbial life. Beyond their scientific value, the polar regions may soon prove important for another reason--providing a valuable and accessible reservoir of water to support the long-term human exploration of Mars. In this paper we assess the current state of Mars polar research, identify the key questions that motivate the exploration of the polar regions, discuss the extent to which current missions will address these questions, and speculate about what additional capabilities and investigations may be required to address the issues that remain outstanding.

Atmosphere↗
PubMed2000

Depositional facies and aqueous-solid geochemistry of travertine-depositing hot springs (Angel Terrace, Mammoth Hot Springs, Yellowstone National Park, U.S.A.).

Petrographic and geochemical analyses of travertine-depositing hot springs at Angel Terrace, Mammoth Hot Springs, Yellowstone National Park, have been used to define five depositional facies along the spring drainage system. Spring waters are expelled in the vent facies at 71 to 73 degrees C and precipitate mounded travertine composed of aragonite needle botryoids. The apron and channel facies (43-72 degrees C) is floored by hollow tubes composed of aragonite needle botryoids that encrust sulfide-oxidizing Aquificales bacteria. The travertine of the pond facies (30-62 degrees C) varies in composition from aragonite needle shrubs formed at higher temperatures to ridged networks of calcite and aragonite at lower temperatures. Calcite "ice sheets", calcified bubbles, and aggregates of aragonite needles ("fuzzy dumbbells") precipitate at the air-water interface and settle to pond floors. The proximal-slope facies (28-54 degrees C), which forms the margins of terracette pools, is composed of arcuate aragonite needle shrubs that create small microterracettes on the steep slope face. Finally, the distal-slope facies (28-30 degrees C) is composed of calcite spherules and calcite "feather" crystals. Despite the presence of abundant microbial mat communities and their observed role in providing substrates for mineralization, the compositions of spring-water and travertine predominantly reflect abiotic physical and chemical processes. Vigorous CO2 degassing causes a +2 unit increase in spring water pH, as well as Rayleigh-type covariations between the concentration of dissolved inorganic carbon and corresponding delta 13C. Travertine delta 13C and delta 18O are nearly equivalent to aragonite and calcite equilibrium values calculated from spring water in the higher-temperature (approximately 50-73 degrees C) depositional facies. Conversely, travertine precipitating in the lower-temperature (< approximately 50 degrees C) depositional facies exhibits delta 13C and delta 18O values that are as much as 4% less than predicted equilibrium values. This isotopic shift may record microbial respiration as well as downstream transport of travertine crystals. Despite the production of H2S and the abundance of sulfide oxidizing microbes, preliminary delta 34S data do not uniquely define the microbial metabolic pathways present in the spring system. This suggests that the high extent of CO2 degassing and large open-system solute reservoir in these thermal systems overwhelm biological controls on travertine crystal chemistry.

Calcium Carbonate↗
PubMed1999

Exploring for a record of ancient Martian life.

The immediate task facing exopaleontology is to define a strategy to explore Mars for a fossil record during the decade-long exploration program that lies ahead. Consideration of the quality of paleontological information preserved under different geological conditions is important if we are to develop a strategy with broad applicability. The preservation of microbial fossils is strongly influenced by the physical, chemical, and biological factors of the environment which, acting together, determine the types of information that will be captured and retained in the rock record. In detrital sedimentary systems, preservation is favored by rapid burial in fine-grained, clay-rich sediments. In chemical sedimentary systems, preservation is enhanced by rapid entombment in fine-grained chemical precipitates. For long-term preservation, host rocks must be composed of stable minerals that are resistant to chemical weathering and that form an impermeable matrix and closed chemical system to protect biosignatures from alteration during subsequent diagenesis or metamorphism. In this context, host rocks composed of highly ordered, chemically stable mineral phases, like silica (e.g., cherts) or phosphate (e.g., phosphorites), are especially favored. Such lithologies tend to have very long crustal residence times and, along with carbonates and shales, are the most common host rocks for the Precambrian microfossil record on Earth. Although we make the defensible assumption that Mars was more like the Earth early in its history, clearly, the geological and historical differences between the two planets are many. Such differences must be carefully considered when adapting an Earth-based strategy to Mars.

Carbonates↗
PubMed1999

Frontiers of finance: evolution and efficient markets.

In this review article, we explore several recent advances in the quantitative modeling of financial markets. We begin with the Efficient Markets Hypothesis and describe how this controversial idea has stimulated a number of new directions of research, some focusing on more elaborate mathematical models that are capable of rationalizing the empirical facts, others taking a completely different tack in rejecting rationality altogether. One of the most promising directions is to view financial markets from a biological perspective and, specifically, within an evolutionary framework in which markets, instruments, institutions, and investors interact and evolve dynamically according to the "law" of economic selection. Under this view, financial agents compete and adapt, but they do not necessarily do so in an optimal fashion. Evolutionary and ecological models of financial markets is truly a new frontier whose exploration has just begun.

Economics↗
PubMed1999

A Mossbauer investigation of iron-rich terrestrial hydrothermal vent systems: lessons for Mars exploration.

Hydrothermal spring systems may well have been present on early Mars and could have served as a habitat for primitive life. The integrated instrument suite of the Athena Rover has, as a component on the robotic arm, a Mossbauer spectrometer. In the context of future Mars exploration we present results of Mossbauer analysis of a suite of samples from an iron-rich thermal spring in the Chocolate Pots area of Yellowstone National Park (YNP) and from Obsidian Pool (YNP) and Manitou Springs, Colorado. We have found that Mossbauer spectroscopy can discriminate among the iron-bearing minerals in our samples. Those near the vent and on the surface are identified as ferrihydrite, an amorphous ferric mineraloid. Subsurface samples, collected from cores, which are likely to have undergone inorganic and/or biologically mediated alteration (diagenesis), exhibit spectral signatures that include nontronite (a smectite clay), hematite (alpha-Fe2O3), small-particle/nanophase goethite (alpha-FeOOH), and siderite (FeCO3). We find for iron minerals that Mossbauer spectroscopy is at least as efficient in identification as X-ray diffraction. This observation is important from an exploration standpoint. As a planetary surface instrument, Mossbauer spectroscopy can yield high-quality spectral data without sample preparation (backscatter mode). We have also used field emission scanning electron microscopy (FESEM), in conjunction with energy-dispersive X ray (EDX) fluorescence spectroscopy, to characterize the microbiological component of surface sinters and the relation between the microbiological and the mineralogical framework. Evidence is presented that the minerals found in these deposits can have multi-billion-year residence times and thus may have survived their possible production in a putative early Martian hot spring up to the present day. Examples include the nanophase property and the Mossbauer signature for siderite, which has been identified in a 2.09-billion-year old hematite-rich chert stromatolite. Our research demonstrates that in situ Mossbauer spectroscopy can help determine whether hydrothermal mineral deposits exist on Mars, which is significant for exobiology because of the issue of whether that world ever had conditions conductive to the origin of life. As a useful tool for selection of samples suitable for transport to Earth, Mossbauer spectroscopy will not only serve geological interests but will also have potential for exopaleontology.

Colorado↗
PubMed1997

Effects of acute and repeated exposures to Aroclor 1254 in adult rats: motor activity and flavor aversion conditioning.

While considerable research has focused on the neurotoxicity of developmental exposures to polychlorinated biphenyls, including Aroclor 1254, relatively little is known about exposures in adult animals. This study investigated the behavioral effects of acute and repeated Aroclor 1254 exposures to adult rats on motor activity and flavor aversion conditioning. Male Long-Evans rats (60 days old) were tested for motor activity in a photocell device after acute (0, 100, 300, or 1000 mg/kg, p.o.) or repeated (0, 1, 3, 10, 30 or 100 mg/kg/day, po, 5 days/week for 4 to 6 weeks exposure to Aroclor 1254. Motor activity was decreased dose-dependently at doses of 300 mg/kg or more after acute exposure. Severe body weight loss and deaths occurred at 1000 mg/kg. Recovery of activity occurred over 9 weeks but was incomplete. After repeated exposure, motor activity was decreased dose-dependently at doses of 30 mg/kg or more, and severe weight loss and deaths occurred at 100 mg/kg. In contrast to acute exposure, complete recovery of activity occurred 3 weeks after exposure. Additional rats were water deprived (30 min/day) and received acute po administration of Aroclor 1254 (0, 10, 15, 25, 30, 100, or 300 mg/kg) shortly after consuming a saccharin solution. Three days later they were given the choice between consuming saccharin or water, and saccharin preferences were recorded. Saccharin preference was decreased at doses of 25 mg/kg or more. Additional experiments determined the effect of repeated saccharin-Aroclor 1254 pairings (0, 3.75, 7.5, or 15 mg/kg/day, 14 days) followed by a choice test 1 day after the last dose. Repeated exposure to 15 mg/kg produced robust flavor aversion conditioning. Repeated exposure to 7.5 mg/kg produced flavor aversion conditioning in four of 12 rats. These results demonstrate that Aroclor 1254 causes hypoactivity and flavor aversions in adult rats; the no observable effect level (NOEL) for motor activity was 100 mg/kg for acute exposure and 10 mg/kg for repeated exposure for a period of up to 6 weeks. The acute NOEL for flavor aversion conditioning was 15 mg/kg while the repeated NOEL was 7.5 mg/kg.

Animals↗
PubMed1996

Hydrothermal systems on Mars: an assessment of present evidence.

Hydrothermal processes have been suggested to explain a number of observations for Mars, including D/H ratios of water extracted from Martian meteorites, as a means for removing CO2 from the Martian atmosphere and sequestering it in the crust as carbonates, and as a possible origin for iron oxide-rich spectral units on the floors of some rifted basins (chasmata). There are numerous examples of Martian channels formed by discharges of subsurface water near potential magmatic heat sources, and hydrothermal processes have also been proposed as a mechanism for aquifer recharge needed to sustain long term erosion of sapping channels. The following geological settings have been identified as targets for ancient hydrothermal systems on Mars: channels located along the margins of impact crater melt sheets and on the slopes of ancient volcanoes; chaotic and fretted terranes where shallow subsurface heat sources are thought to have interacted with ground ice; and the floors of calderas and rifted basins (e.g. chasmata). On Earth, such geological environments are often a locus for hydrothermal mineralization. But we presently lack the mineralogical information needed for a definitive evaluation of hypotheses. A preferred tool for identifying minerals by remote sensing methods on Earth is high spatial resolution, hyperspectral, near-infrared spectroscopy, a technique that has been extensively developed by mineral explorationists. Future efforts to explore Mars for ancient hydrothermal systems would benefit from the application of methods developed by the mining industry to look for similar deposits on Earth. But Earth-based exploration models must be adapted to account for the large differences in the climatic and geological history of Mars. For example, it is likely that the early surface environment of Mars was cool, perhaps consistently below freezing, with the shallow portions of hydrothermal systems being dominated by magma-cryosphere interactions. Given the smaller gravitational field, declining atmospheric pressure, and widespread, permeable megaregolith on Mars, volatile outgassing and magmatic cooling would have been more effective than on Earth. Thus, hydrothermal systems are likely to have had much lower average surface temperatures than comparable geological settings on Earth. The likely predominance of basaltic crust on Mars suggests that hydrothermal fluids and associated deposits should be enriched in Fe, Mg, Si and Ca, with surficial deposits being dominated by lower temperature, mixed iron oxide and carbonate mineralogies.

Deuterium↗
PubMed1996

Fossilization processes in siliceous thermal springs: trends in preservation along thermal gradients.

To enhance our ability to extract palaeobiological and palaeoenvironmental information from ancient thermal spring deposits, we have studied the processes responsible for the development and preservation of stromatolites in modern subaerial thermal spring systems in Yellowstone National Park (USA). We investigated specimens collected from silica-depositing thermal springs along the thermal gradient using petrographic techniques and scanning electron microscopy. Although it is known that thermophilic cyanobacteria control the morphogenesis of thermal spring stromatolites below 73 degrees C, we have found that biofilms which contain filamentous thermophiles contribute to the microstructural development of subaerial geyserites that occur along the inner rims of thermal spring pools and geyser effluents. Biofilms intermittently colonize the surfaces of subaerial geyserites and provide a favoured substrate for opaline silica precipitation. We have also found that the preservation of biotically produced microfabrics of thermal spring sinters reflects dynamic balances between rates of population growth, decomposition of organic matter, silica deposition and early diagenesis. Major trends in preservation of thermophilic organisms along the thermal gradient are defined by differences in the mode of fossilization, including replacement, encrustation and permineralization.

Bacteria↗
PubMed1996

Relationship between structure and biological activity of novel R106 analogs.

The retro-aldol reaction at residue 8 of R106-1 produced a chemical handle, in the form of a sarcosine residue, that was amenable to classical aldol alkylation conditions. In vitro assay of several new hydroxylated analogs have shown that L isomers exhibit more potent antifungal activity than D isomers. However, all analogs exhibited a significant decrease in activity against Cryptococcus neoformans. By contrast, structural modifications of R 106 were tolerated by some Candida spp., but the potency of activity was diminished as compared to that of the natural product R106-1. The full structure-activity relationship of the new R106 analogs has provided important information about the steric and electronic requirements of binding to target receptors. Furthermore, comparison of the structural differences between R106-1 and other derivatives, suggested that the potential for hydrogen bonding (at residue 8) was a key structural feature that was required to maintain activity against Cryptococcus neoformans.

Anti-Bacterial Agents↗
PubMed1996

Lithofacies and biofacies of mid-Paleozoic thermal spring deposits in the Drummond Basin, Queensland, Australia.

The Devonian to Carboniferous sinters of the Drummond Basin, Australia, are among the oldest well established examples of fossil subaerial hot springs. Numerous subaerial and subaqueous spring deposits are known from the geological record as a result of the occurrence of economic mineral deposits in many of them. Some are reported to contain fossils, but very few have been studied by paleobiologists; they represent an untapped source of paleobiological information on the history of hydrothermal ecosystems. Such systems are of special interest, given the molecular biological evidence that thermophilic bacteria lie near the root of the tree of extant life. The Drummond Basin sinters are very closely comparable with modern examples in Yellowstone National Park and elsewhere. Thirteen microfacies are recognisable in the field, ranging from high temperature apparently abiotic geyserite through various forms of stromatolitic sinter probably of cyanobacterial origin to ambient temperature marsh deposits. Microfossils in the stromatolites are interpreted as cyanobacterial sheaths. Herbaceous lycopsids occur in the lower temperature deposits.

Australia↗
PubMed1993

Radiocarbon ages of lacustrine deposits in volcanic sequences of the Lomas Coloradas area, Socorro Island, Mexico.

Extensive eruptions of alkalic basalt from low-elevation fissures and vents on the southern flank of the dormant volcano, Cerro Evermann, accompanied the most recent phase of volcanic activity on Socorro Island, and created the Lomas Coloradas, a broad, gently sloping terrain comprising the southern part of the island. We obtained 14C ages of 4690 +/- 270 BP (5000-5700 cal BP) and 5040 +/- 460 BP (5300-6300 cal BP) from lacustrine deposits that occur within volcanic sequences of the lower Lomas Coloradas. Apparently, the sediments accumulated within a topographic depression between two scoria cones shortly after they formed. The lacrustine environment was destroyed when the cones were breached by headward erosion of adjacent stream drainages. This was followed by the eruption of a thin basaltic flow from fissures near the base of the northernmost cone. The flow moved downslope for a short distance and into the drainages that presently bound the study area on the east and west. The flow postdates development of the present drainage system and may be very recent. Our 14C data, along with historical accounts of volcanic activity over the last century, including submarine eruptions that occurred a few km west of Socorro in early 1993, underscore the high risk for explosive volcanism in this region and the need for a detailed volcanic hazards plan and seismic monitoring.

Carbon Radioisotopes↗
PubMed1991

Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes.

Although the immediate receptors (immunophilins) of the immunosuppressants cyclosporin A (CsA) and FK506 are distinct, their similar mechanisms of inhibition of cell signaling suggest that their associated immunophilin complexes interact with a common target. We report here that the complexes cyclophilin-CsA and FKBP-FK506 (but not cyclophilin, FKBP, FKBP-rapamycin, or FKBP-506BD) competitively bind to and inhibit the Ca(2+)- and calmodulin-dependent phosphatase calcineurin, although the binding and inhibition of calcineurin do not require calmodulin. These results suggest that calcineurin is involved in a common step associated with T cell receptor and IgE receptor signaling pathways and that cyclophilin and FKBP mediate the actions of CsA and FK506, respectively, by forming drug-dependent complexes with and altering the activity of calcineurin-calmodulin.

Amino Acid Isomerases↗
PubMed1991

DNA binding properties of a new class of linked anthramycin analogs.

We have investigated the DNA binding properties of the anthramycin analogues 4, 5, and 6 using fluorescence spectroscopy. A considerable fluorescence enhancement occurs when pyrrolo [1,4] benzodiazepines (P[1,4]Bs) are covalently attached to duplex DNA, which was used to show that neither the presence of RNA, single-stranded DNA, or protein had any effect on the degree of fluorescence enhancement resulting from the incubation of 5 and 6 with DNA. The enhancement was found to be dependent on the presence of the imine functionality in each of the compounds. A wavelength of 320 nm was used to excite the chromophore and its emission wavelength maximum was 420 nm. Additionally, we have discovered that the P[1,4]B ring system exhibits exceptionally favorable fluorescence polarization anisotropy (FPA) decay characteristics. For these more detailed fluorescence measurements, we used the structurally simpler analogue 4,. The time resolved maximum FPA for 4 in glycerol at 25 degrees C is 0.28. This result indicates that the P[1,4]B family of antibiotics could serve as sensitive probes of DNA dynamics in the 0.1 to 35 ns time scale.

Animals↗
PubMed1989

Time-dependent deficits in delay conditioning produced by trimethyltin.

Trimethyltin (TMT) produces behavioral and cognitive deficits resulting, in part, from limbic system toxicity. To determine whether these effects result from learning deficits or accelerated memory loss, the present experiment examined two delay conditioning paradigms in rats previously treated with either saline or TMT. Saline-treated Long-Evans rats receiving injections of lithium after consuming saccharin-flavored water later avoided saccharin ingestion: the degree of avoidance varied inversely with the time (0.5, 3 or 6 h) separating initial saccharin availability and lithium injection. Rats treated with TMT (8 mg/kg IV, 30 days prior) showed impaired conditioning at the long but not the short or intermediate delay conditions, suggesting that the deficits were mnemonic and not associative. Similar delay-dependent deficits in rats treated with TMT were observed in a passive avoidance task that arranged one of two delays between response emission and shock delivery during training. The effects of TMT on delay conditioning were accompanied by reduced bodyweight and hippocampal pathology. In summary, TMT appears to alter the temporally dependent association of events (entering darkened compartment versus saccharin consumption) and consequences (foot shock versus lithium administration) during acquisition. Furthermore, the observed deficits in delay conditioning produced by TMT did not appear to be task specific, with similar effects determined with tests of both somatosensory and gustatory avoidance learning designed to distinguish between functional alterations due to deficits in memorial processes from those due to altered sensory, motor, or associative processes.

Animals↗
PubMed1989

Modeling adaptive biological systems.

During the evolution of many systems found in nature, both the system composition and the interactions between components will vary. Equating the dimension with the number of different components, a system which adds or deletes components belongs to a class of dynamical systems with a finite dimensional phase space of variable dimension. We present two models of biochemical systems with a variable phase space, a model of autocatalytic reaction networks in the prebiotic soup and a model of the idiotypic network of the immune system. Each model contains characteristic meta-dynamical rules for constructing equations of motion from component properties. The simulation of each model occurs on two levels. On one level, the equations of motion are integrated to determine the state of each component. On a second level, algorithms which approximate physical processes in the real system are employed to change the equations of motion. Models with meta-dynamical rules possess several advantages for the study of evolving systems. First, there are no explicit fitness functions to determine how the components of the model rank in terms of survivability. The success of any component is a function of its relationship to the rest of the system. A second advantage is that since the phase space representation of the system is always finite but continually changing, we can explore a potentially infinite phase space which would otherwise be inaccessible with finite computer resources. Third, the enlarged capacity of systems with meta-dynamics for variation allows us to conduct true evolution experiments. The modeling methods presented here can be applied to many real biological systems. In the two studies we present, we are investigating two apparent properties of adaptive networks. With the simulation of the prebiotic soup, we are most interested in how a chemical reaction network might emerge from an initial state of relative disorder. With the study of the immune system, we study the self-regulation of the network including its ability to distinguish between species which are part of the network and those which are not.

Adaptation, Biological↗