Instrumental Perspectivism: Is AI Machine Learning Technology like NMR Spectroscopy?

The question, “Will science remain human?” expresses a worry that deep learning algorithms will replace scientists in making crucial judgments of classification and inference and that something crucial will be lost if that happens.  Ever since the introduction of telescopes and microscopes humans have relied on technologies to “extend” beyond human sensory perception in acquiring scientific knowledge.  In this paper I explore whether the ways in which new learning technologies “extend” beyond human cognitive aspects of science can be treated instrumentally. I will consider the norms for determining the reliability of a detection instrument, nuclear magnetic resonance spectroscopy, in predicting models of protein atomic structure. Do the same norms that apply in that case be used to judge the reliability of Artificial Intelligence deep learning algorithms

Integrated Carbon Budget Models for the Everglades Terrestrial-Coastal-Oceanic Gradient: Current Status and Needs for Inter-Site Comparisons

Recent studies suggest that coastal ecosystems can bury significantly more C than tropical forests, indicating that continued coastal development and exposure to sea level rise and storms will have global biogeochemical consequences. The Florida Coastal Everglades Long Term Ecological Research (FCE LTER) site provides an excellent subtropical system for examining carbon (C) balance because of its exposure to historical changes in freshwater distribution and sea level rise and its history of significant long-term carbon-cycling studies. FCE LTER scientists used net ecosystem C balance and net ecosystem exchange data to estimate C budgets for riverine mangrove, freshwater marsh, and seagrass meadows, providing insights into the magnitude of C accumulation and lateral aquatic C transport. Rates of net C production in the riverine mangrove forest exceeded those reported for many tropical systems, including terrestrial forests, but there are considerable uncertainties around those estimates due to the high potential for gain and loss of C through aquatic fluxes. C production was approximately balanced between gain and loss in Everglades marshes; however, the contribution of periphyton increases uncertainty in these estimates. Moreover, while the approaches used for these initial estimates were informative, a resolved approach for addressing areas of uncertainty is critically needed for coastal wetland ecosystems. Once resolved, these C balance estimates, in conjunction with an understanding of drivers and key ecosystem feedbacks, can inform cross-system studies of ecosystem response to long-term changes in climate, hydrologic management, and other land use along coastlines

Fruit crops: a summary of research, 1998

Pesticide deposition in orchards: effects of pesticide type, tree canopy, timing, cultivar, and leaf type / Franklin R. Hall, Jane A. Cooper, and David C. Ferree -- The influence of a synthetic foraging attractant, Bee-Scent™, on the number of honey bees visiting apple blossoms and on subsequent fruit production / James E. Tew and David C. Ferree -- The reliability of three traps vs. a single trap for determining population levels of codling moth in commercial northern Ohio apple orchards / Ted W. Gastier -- Evaluation of an empirical model for predicting sooty blotch and flyspeck of apples in Ohio / Michael A. Ellis, Laurence V. Madden, and L. Lee Wilson -- Influence of pesticides and water stress on photosynthesis and transpiration of apple / David C. Ferree, Franklin R. Hall, Charles R. Krause, Bruce R. Roberts, and Ross D. Brazee -- Influence of temporary bending and heading on branch development and flowering of vigorous young apple trees / David C. Ferree and John C. Schmid -- The effect of apple fruit bruising on total returns / Richard C. Funt, Ewen A. Cameron, and Nigel H. Banks -- Yield, berry quality, and economics of mechanical berry harvest in Ohio / Richard C. Funt, Thomas E. Wall, and Joseph C. Scheerens -- Monitoring flower thrips activities in strawberry fields at two Ohio locations / Roger N. Williams, M. Sean Ellis, Dan S. Fickle, and Carl M. Pelland -- Cluster thinning effects on fruit weight, juice quality, and fruit skin characteristics in 'Reliance' grapes / Yu Gao and Garth A. Cahoon -- Effects of various fungicide programs on powdery mildew control, percent berry sugar, yield, and vine vigor of 'Concord' grapes in Ohio / Michael A. Ellis, Laurence V. Madden, L. Lee Wilson, and Gregory R. Johns -- Influence of growth regulators, cropping, and number on replacement trunks of winter-injured 'Vidal Blanc' grapes / David C. Ferree, David M. Scurlock, and Rick Evans -- Effect of new herbicides on tissue-cultured black raspberry plants / Richard C. Funt, Thomas E. Wall, and B. Dale Stokes -- Investigating the relationship between vine vigor and berry set of field-grown 'Seyval Blanc' grapevines / Steven J. McArtney and David C. Ferree -- Summary of Ohio Fruit Growers Society apple cider competition, 1993-1997 / Winston Bash and Diane Mille

PDRs4All IV. An embarrassment of riches: Aromatic infrared bands in the Orion Bar

(Abridged) Mid-infrared observations of photodissociation regions (PDRs) are dominated by strong emission features called aromatic infrared bands (AIBs). The most prominent AIBs are found at 3.3, 6.2, 7.7, 8.6, and 11.2 $\mu$m. The most sensitive, highest-resolution infrared spectral imaging data ever taken of the prototypical PDR, the Orion Bar, have been captured by JWST. We provide an inventory of the AIBs found in the Orion Bar, along with mid-IR template spectra from five distinct regions in the Bar: the molecular PDR, the atomic PDR, and the HII region. We use JWST NIRSpec IFU and MIRI MRS observations of the Orion Bar from the JWST Early Release Science Program, PDRs4All (ID: 1288). We extract five template spectra to represent the morphology and environment of the Orion Bar PDR. The superb sensitivity and the spectral and spatial resolution of these JWST observations reveal many details of the AIB emission and enable an improved characterization of their detailed profile shapes and sub-components. While the spectra are dominated by the well-known AIBs at 3.3, 6.2, 7.7, 8.6, 11.2, and 12.7 $\mu$m, a wealth of weaker features and sub-components are present. We report trends in the widths and relative strengths of AIBs across the five template spectra. These trends yield valuable insight into the photochemical evolution of PAHs, such as the evolution responsible for the shift of 11.2 $\mu$m AIB emission from class B$_{11.2}$ in the molecular PDR to class A$_{11.2}$ in the PDR surface layers. This photochemical evolution is driven by the increased importance of FUV processing in the PDR surface layers, resulting in a "weeding out" of the weakest links of the PAH family in these layers. For now, these JWST observations are consistent with a model in which the underlying PAH family is composed of a few species: the so-called 'grandPAHs'.Comment: 25 pages, 10 figures, to appear in A&

A far-ultraviolet-driven photoevaporation flow observed in a protoplanetary disk

Most low-mass stars form in stellar clusters that also contain massive stars, which are sources of far-ultraviolet (FUV) radiation. Theoretical models predict that this FUV radiation produces photo-dissociation regions (PDRs) on the surfaces of protoplanetary disks around low-mass stars, impacting planet formation within the disks. We report JWST and Atacama Large Millimetere Array observations of a FUV-irradiated protoplanetary disk in the Orion Nebula. Emission lines are detected from the PDR; modelling their kinematics and excitation allows us to constrain the physical conditions within the gas. We quantify the mass-loss rate induced by the FUV irradiation, finding it is sufficient to remove gas from the disk in less than a million years. This is rapid enough to affect giant planet formation in the disk

PDRs4All III: JWST's NIR spectroscopic view of the Orion Bar

(Abridged) We investigate the impact of radiative feedback from massive stars on their natal cloud and focus on the transition from the HII region to the atomic PDR (crossing the ionisation front (IF)), and the subsequent transition to the molecular PDR (crossing the dissociation front (DF)). We use high-resolution near-IR integral field spectroscopic data from NIRSpec on JWST to observe the Orion Bar PDR as part of the PDRs4All JWST Early Release Science Program. The NIRSpec data reveal a forest of lines including, but not limited to, HeI, HI, and CI recombination lines, ionic lines, OI and NI fluorescence lines, Aromatic Infrared Bands (AIBs including aromatic CH, aliphatic CH, and their CD counterparts), CO2 ice, pure rotational and ro-vibrational lines from H2, and ro-vibrational lines HD, CO, and CH+, most of them detected for the first time towards a PDR. Their spatial distribution resolves the H and He ionisation structure in the Huygens region, gives insight into the geometry of the Bar, and confirms the large-scale stratification of PDRs. We observe numerous smaller scale structures whose typical size decreases with distance from Ori C and IR lines from CI, if solely arising from radiative recombination and cascade, reveal very high gas temperatures consistent with the hot irradiated surface of small-scale dense clumps deep inside the PDR. The H2 lines reveal multiple, prominent filaments which exhibit different characteristics. This leaves the impression of a "terraced" transition from the predominantly atomic surface region to the CO-rich molecular zone deeper in. This study showcases the discovery space created by JWST to further our understanding of the impact radiation from young stars has on their natal molecular cloud and proto-planetary disk, which touches on star- and planet formation as well as galaxy evolution.Comment: 52 pages, 30 figures, submitted to A&

PDRs4All II: JWST's NIR and MIR imaging view of the Orion Nebula

The JWST has captured the most detailed and sharpest infrared images ever taken of the inner region of the Orion Nebula, the nearest massive star formation region, and a prototypical highly irradiated dense photo-dissociation region (PDR). We investigate the fundamental interaction of far-ultraviolet photons with molecular clouds. The transitions across the ionization front (IF), dissociation front (DF), and the molecular cloud are studied at high-angular resolution. These transitions are relevant to understanding the effects of radiative feedback from massive stars and the dominant physical and chemical processes that lead to the IR emission that JWST will detect in many Galactic and extragalactic environments. Due to the proximity of the Orion Nebula and the unprecedented angular resolution of JWST, these data reveal that the molecular cloud borders are hyper structured at small angular scales of 0.1-1" (0.0002-0.002 pc or 40-400 au at 414 pc). A diverse set of features are observed such as ridges, waves, globules and photoevaporated protoplanetary disks. At the PDR atomic to molecular transition, several bright features are detected that are associated with the highly irradiated surroundings of the dense molecular condensations and embedded young star. Toward the Orion Bar PDR, a highly sculpted interface is detected with sharp edges and density increases near the IF and DF. This was predicted by previous modeling studies, but the fronts were unresolved in most tracers. A complex, structured, and folded DF surface was traced by the H2 lines. This dataset was used to revisit the commonly adopted 2D PDR structure of the Orion Bar. JWST provides us with a complete view of the PDR, all the way from the PDR edge to the substructured dense region, and this allowed us to determine, in detail, where the emission of the atomic and molecular lines, aromatic bands, and dust originate

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Rare and low-frequency coding variants alter human adult height

Height is a highly heritable, classic polygenic trait with ~700 common associated variants identified so far through genome - wide association studies . Here , we report 83 height - associated coding variants with lower minor allele frequenc ies ( range of 0.1 - 4.8% ) and effects of up to 2 16 cm /allele ( e.g. in IHH , STC2 , AR and CRISPLD2 ) , >10 times the average effect of common variants . In functional follow - up studies, rare height - increasing alleles of STC2 (+1 - 2 cm/allele) compromise d proteolytic inhibition of PAPP - A and increased cleavage of IGFBP - 4 in vitro , resulting in higher bioavailability of insulin - like growth factors . The se 83 height - associated variants overlap genes mutated in monogenic growth disorders and highlight new biological candidates ( e.g. ADAMTS3, IL11RA, NOX4 ) and pathways ( e.g . proteoglycan/ glycosaminoglycan synthesis ) involved in growth . Our results demonstrate that sufficiently large sample sizes can uncover rare and low - frequency variants of moderate to large effect associated with polygenic human phenotypes , and that these variants implicate relevant genes and pathways