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Processing predictive relationships in sequential auditory input is a core capacity allowing for the emergence of syntax., Rawski et al. revisit our recent findings suggesting the latent ability to process nonadjacent dependencies (“Non-ADs”) in monkeys and apes. Specifically, the authors question the relevance of our findings for the evolution of human syntax. We argue that (i) these conclusions hinge upon an assumption that language processing is necessarily hierarchical, which remains an open question, and (ii) our goal was to probe the foundational cognitive mechanisms facilitating the processing of syntactic Non-ADs—namely, the ability to recognize predictive relationships in the input.

Evidence shows that animals match humans when learning sound patterns but not sentence patterns., We comment on the technical interpretation of the study of Watson et al. and caution against their conclusion that the behavioral evidence in their experiments points to nonhuman animals’ ability to learn syntactic dependencies, because their results are also consistent with the learning of phonological dependencies in human languages.

The article by Fan et al. inaccurately states that ProPerDP is inadequate for protein persulfide detection., The recent report by Fan et al. alleged that the ProPerDP method is inadequate for the detection of protein persulfidation. Upon careful evaluation of their work, we conclude that the claim made by Fan et al. is not supported by their data, rather founded in methodological shortcomings. It is understood that the ProPerDP method generates a mixture of cysteine-containing and non–cysteine-containing peptides. Instead, Fan et al. suggested that the detection of non–cysteine-containing peptides indicates nonspecific alkylation at noncysteine residues. However, if true, then such peptides would not be released by reduction and therefore not appear as products in the reported workflow. Moreover, the authors’ biological assessment of ProPerDP using Escherichia coli mutants was based on assumptions that have not been confirmed by other methods. We conclude that Fan et al. did not rigorously assess the method and that ProPerDP remains a reliable approach for analyses of protein per/polysulfidation.

A Science Advances paper concluding that GREs do not predict who will get a physics Ph.D. has many statistical errors., A recent paper in Science Advances by Miller et al. concludes that Graduate Record Examinations (GREs) do not help predict whether physics graduate students will get Ph.D.’s. Here, I argue that the presented analyses reflect collider-like stratification bias, variance inflation by collinearity and range restriction, omission of parts of a needed correlation matrix, a peculiar choice of null hypothesis on subsamples, blurring the distinction between failure to reject a null and accepting a null, and an unusual procedure that inflates the confidence intervals in a figure. Release of results of a model that leaves out stratification by the rank of the graduate program would fix many of the problems.

Additional analysis confirms that GRE-Q and GRE-P scores have limited reliability in predicting Ph.D. completion in physics., We provide statistical measures and additional analyses showing that our original analyses were sound. We use a generalized linear mixed model to account for program-to-program differences with program as a random effect without stratifying with tier and found the GRE-P (Graduate Record Examination physics test) effect is not different from our previous findings, thereby alleviating concern of collider bias. Variance inflation factors for each variable were low, showing that multicollinearity was not a concern. We show that range restriction is not an issue for GRE-P or GRE-V (GRE verbal), and only a minor issue for GRE-Q (GRE quantitative). Last, we use statistical measures of model quality to show that our published models are better than or equivalent to several alternates.

6-N-hydroxylaminopurine produced by the commensal skin bacterium Staphylococcus epidermidis MO34 is strongly mutagenic., A recent article in Science Advances described the striking discovery that the commensal Staphylococcus epidermidis strain MO34 displays antimicrobial and antitumor activities by producing a small molecule, identified as the nucleobase analog 6-N-hydroxylaminopurine (6-HAP). However, in contradiction to the literature, the authors claimed that 6-HAP is nonmutagenic and proposed that the toxic effect of 6-HAP results from its ability to inhibit, in its base form, DNA synthesis. To resolve the discrepancy, we proved by genetic experiments with bacteria and yeast that extracts of MO34 do contain a mutagenic compound whose effects are identical to chemically synthesized 6-HAP. The MO34 extract induced the same mutation spectrum as authentic 6-HAP. Notably, the toxic and mutagenic effects of both synthetic and MO34-derived 6-HAP depended on conversion to the corresponding nucleotide. The nucleobase 6-HAP does not inhibit DNA synthesis in vitro, and we conclude that 6-HAP exerts its biological activity when incorporated into DNA.

Does a wet winter recharge deep aquifers in California?, In a study by Murray and Lohman (M&L), the authors suggest that remote sensing data are useful for monitoring land subsidence due to aquifer system compaction. We agree. To infer aquifer dynamics, we provide a more detailed and joint analysis of deformation and groundwater data. Investigating well data in the Tulare Basin, we find that groundwater levels stabilized before 2015 and show that M&L’s observed continued subsidence through July 2016 is likely caused by the delayed compaction of the aquitard. Our analysis suggests the observed 2017 transient uplift is not due to recharge of the aquifer system after heavy winter rainfall because it requires an unrealistic vertical hydraulic gradient nearly five orders of magnitude larger than that typical of Tulare Basin. We find that, regardless of the amount of rainfall, transient annual uplifts of ~3 cm occur in May to June. Using an elastic skeletal storage coefficient of 5 × 10−3, we link this ground uplift to annual groundwater level changes.

Failed attempts to reproduce measurements suffer from lower resolution not ghosts., Gehring et al. argue that a splitting observed by us in the transverse acoustic (TA) phonon in the relaxor ferroelectric Pb[(Mg1/3Nb2/3)1−xTix]O3 with x = 0.30 (PMN-30PT) is caused by a combination of inelastic-elastic multiple scattering processes called ghostons. Their argument is motivated by differences observed between their measurements made on a triple-axis spectrometer and our measurements on a time-of-flight spectrometer. We show that the differences can be explained by differences in the instrument resolution functions. We demonstrate that the multiple scattering conditions proposed by Gehring et al. do not work for our scattering geometry. We also show that, when a ghoston is present, it is too weak to detect and therefore cannot explain the splitting. Last, this phonon splitting is just one part of the argument, and the overall conclusion of the original paper is supported by other results.

Phantom indications of phonon anticrossing in relaxor ferroelectrics can arise via an inelastic double-scattering process., Manley et al. (Science Advances, 16 September 2016, p. e1501814) report the splitting of a transverse acoustic phonon branch below TC in the relaxor ferroelectric Pb[(Mg1/3Nb2/3)1−xTix]O3 with x = 0.30 using neutron scattering methods. Manley et al. argue that this splitting occurs because these phonons hybridize with local, harmonic lattice vibrations associated with polar nanoregions. We show that splitting is absent when the measurement is made using a different neutron wavelength, and we suggest an alternative interpretation.

Canadian and U.S. wildlife management needs an improved scientific basis and clearer definition of “science-based” expectations., Mawdsley et al. (2018) respond disapprovingly to our 2018 review of 667 wildlife management systems across Canada and the United States, which found that many of these systems lacked the scientific hallmarks of clear objectives, evidence, transparency, and independent review. Although we strongly agree with several of Mawdsley et al.’s points about the role of science in management, their response suggests confusion about three elements of our approach that we clarify herein: (i) the selection of hallmarks, (ii) the role of science in wildlife management, and (iii) our engagement with wildlife agencies. We contend that both critics and defenders of the current approach to wildlife management in Canada and the United States similarly desire rigorous management that achieves social and ecological benefits. Our original study—which used a clear approach to define hallmarks of science-based management, employed a reasonable set of indicator criteria to test for them, and was based on data available to the general public on whose behalf management is conducted—found evidence that the current approach falls short. However, it also provided a framework for addressing shortcomings moving forward. We suggest that advancing discussion on the operational role of science in management, including clarifying what “science-based management” actually means, could curtail practitioners and critics of the status quo talking over each other’s heads and encourage all parties to work constructively to improve the governance of wildlife at a continental scale.

Biogeochemical models are more capable of capturing statewide soil NOx emissions than emission factors., Maaz et al. argue that inconsistencies across scales of observation undermine our working hypothesis that soil NOx emissions have been substantially overlooked in California; however, the core issues they raise are already discussed in our manuscript. We agree that point measurements cannot be reliably used to estimate statewide soil NOx emissions—the principal motivation behind our new modeling/airplane approach. Maaz et al.’s presentation of fertilizer-based emission factors (a nonmechanistic scaling of point measures to regions based solely on estimated nitrogen fertilizer application rates) includes no data from California or other semiarid sites, and does not explicitly account for widely known controls of climate, soil, and moisture on soil NOx fluxes. In contrast, our model includes all of these factors. Finally, the fertilizer sales data that Maaz et al. highlight are known to suffer from serious errors and do not offer a logically more robust pathway for spatial analysis of NOx emissions from soil.

Several inconsistencies undermine the conclusion that agricultural soils are a dominant source of NOx pollution in California., Almaraz et al. reported that agricultural soils are a dominant source of NOx pollution in California (20 to 32% of total statewide NOx emissions). However, this conclusion may be undermined by the lack of agreement between their modeled estimates and previously reported empirical measurements, the extrapolation of NOx fluxes during hot moments to derive annual estimates, and the overestimation of nitrogen fertilizer consumption in California.

Kondash et al. incorrectly claim that water intensity has increased in all regions, and several data errors are apparent., Kondash et al. provide a valuable contribution to our understanding of water consumption and wastewater production from oil and gas production using hydraulic fracturing. Unfortunately, their claim that the water intensity of energy production using hydraulic fracturing has increased in all regions is incorrect. More comprehensive data show that, while the water intensity of production may have increased in regions such as the Permian basin, it has decreased by 74% in the Marcellus and by 19% in the Eagle Ford region. This error likely stems from an improper method for estimating energy production from wells: The authors use the median well to represent regional production, which systematically underestimates aggregate production volumes. Across all regions, aggregate data suggest that the water intensity of oil and natural gas production using hydraulic fracturing has increased by 19%. There also appears to be an error in estimates for water consumption in the Permian basin.

Estimates of seismic response to injection rate reduction in Oklahoma are model-dependent and remain uncertain in 2017 and beyond., The state of Oklahoma has experienced an unprecedented increase in earthquake activity since 2009, likely driven by large-scale wastewater injection operations. Statewide injection rates peaked in early 2015 and steadily decreased thereafter, approximately coinciding with collapsing oil prices and regulatory action. If seismic activity is primarily driven by fluid injection, a noticeable seismogenic response to the decrease in injection rates is expected. Langenbruch and Zoback suggest that “the probability of potentially damaging larger events, should significantly decrease by the end of 2016 and approach historic levels within a few years.” We agree that the rate of small earthquakes has decreased toward the second half of 2016. However, their specific predictions about seismic hazard require reexamination. We test the influence of the model parameters of Langenbruch and Zoback based on fits to observed seismicity distributions. The results suggest that a range of realistic aftershock decay rates and b values can lead to an increase in moderate earthquake probabilities from 37 to 80% in 2017 without any further alteration to the model. In addition, the observation that all four M ≥ 5 earthquakes to date occurred when injection rates were below the triggering threshold of Langenbruch and Zoback challenges the applicability of the model for the most societally significant events.

Fundamental components of science are often lacking in U.S. state and Canadian provincial hunt management systems., Resource management agencies commonly defend controversial policy by claiming adherence to science-based approaches. For example, proponents and practitioners of the “North American Model of Wildlife Conservation,” which guides hunting policy across much of the United States and Canada, assert that science plays a central role in shaping policy. However, what that means is rarely defined. We propose a framework that identifies four fundamental hallmarks of science relevant to natural resource management (measurable objectives, evidence, transparency, and independent review) and test for their presence in hunt management plans created by 62 U.S. state and Canadian provincial and territorial agencies across 667 management systems (species-jurisdictions). We found that most (60%) systems contained fewer than half of the indicator criteria assessed, with more criteria detected in systems that were peer-reviewed, that pertained to “big game,” and in jurisdictions at increasing latitudes. These results raise doubt about the purported scientific basis of hunt management across the United States and Canada. Our framework provides guidance for adopting a science-based approach to safeguard not only wildlife but also agencies from potential social, legal, and political conflict.

We discuss possible mechanisms to explain paleoclimate as a predictor of the current distribution of global soil C content., The technical comment from Sanderman provides a unique opportunity to deepen our understanding of the mechanisms explaining the role of paleoclimate in the contemporary distribution of global soil C content, as reported in our article. Sanderman argues that the role of paleoclimate in predicting soil C content might be accounted for by using slowly changing soil properties as predictors. This is a key point that we highlighted in the supplementary materials of our article, which demonstrated, to the degree possible given available data, that soil properties alone cannot account for the unique portion of the variation in soil C explained by paleoclimate. Sanderman also raised an interesting question about how paleoclimate might explain the contemporary amount of C in our soils if such a C is relatively new, particularly in the topsoil layer. There is one relatively simple, yet plausible, reason. A soil with a higher amount of C, a consequence of accumulation over millennia, might promote higher contemporary C fixation rates, leading to a higher amount of new C in our soils. Thus, paleoclimate can be a good predictor of the amount of soil C in soil, but not necessarily of its age. In summary, Sanderman did not question the validity of our results but rather provides an alternative potential mechanistic explanation for the conclusion of our original article, that is, that paleoclimate explains a unique portion of the global variation of soil C content that cannot be accounted for by current climate, vegetation attributes, or soil properties.

Genome sequence and ancestry analysis confirm only two canid species in North America., A response to Hohenlohe et al.

We thank P. Lieberman for his technical comment, and we are pleased that he accepts our data, methods, and results and agrees with our main conclusion: that a macaque’s vocal tract would be able to produce speech sounds if macaques had the required neural control. However, we cannot agree that our findings, which expand the phonetic potential of macaques eightfold relative to that reported in his seminal 1969 paper, in any sense constitute a “replication” of that study or demonstrate the correctness of his earlier conclusions. To recap, both studies used measurements of macaque monkey vocal tracts to create a computer model, which was then queried to determine what vocalizations it could potentially produce: a space representing the “phonetic potential” of that vocal tract. The key difference between the two studies is that our vocal tract measurements were derived from x-rays of living monkeys vocalizing and communicating ( 1 ), whereas the measurements of Lieberman et al . [( 2 ), p. 1186] were derived from a single cast of a dead monkey, with possible perturbations “estimated” by “manipulating … an anesthetized monkey.” We believe that this difference in the quality of the input data is responsible for the key difference in our results: an eightfold increase in the macaque phonetic potential as estimated by our model [see our Fig. 3 in ( 1 )]. Going beyond Lieberman’s original study, we also generated five “monkey vowels” that optimally partitioned this enlarged acoustic space. Perceptual experiments then showed that humans readily discriminate between these five vowels. Five vowels were chosen because that is the modal number of vowels in human languages around the world, although the specific vowels vary, of course, from language to language ( 3 , 4 ). Given that nonhuman primate formant perception is very similar to that of humans ( 5 , 6 ), this finding …

DMS odors on plastic debris may not explain plastic ingestion by seabirds., In their recent paper, Savoca and collaborators (2016) showed that plastic debris in the ocean may acquire a dimethyl sulfide (DMS) signature from biofouling developing on their surface. According to them, DMS emission may represent an olfactory trap for foraging seabirds, which explains patterns of plastic ingestion among procellariiform seabirds. This hypothesis is appealing, but some of the data that Savoca et al. used to support their claim are questionable, resulting in a misclassification of species, as well as other decisions regarding the variables to include in their models. Furthermore, with their focus on a single lifestyle trait (nesting habit) of dubious relevance for explaining plastic ingestion, Savoca et al. neglect the opportunity to explore other factors that might provide better ecological insight. Finally, we are deeply concerned by the conservation policy recommendation proposed by Savoca et al.—to increase antifouling properties of consumer plastics—which constitutes a substantial environmental risk and delivers the wrong message to decision-makers. The reduction of plastic consumption, waste prevention, and proactive reuse through a circular economy should be at the heart of policy recommendations for future mitigation efforts.

X-ray analyses of macaque vocal tract movements show that monkeys’ inability to speak is not due to limitations of peripheral anatomy., For four decades, the inability of nonhuman primates to produce human speech sounds has been claimed to stem from limitations in their vocal tract anatomy, a conclusion based on plaster casts made from the vocal tract of a monkey cadaver. We used x-ray videos to quantify vocal tract dynamics in living macaques during vocalization, facial displays, and feeding. We demonstrate that the macaque vocal tract could easily produce an adequate range of speech sounds to support spoken language, showing that previous techniques based on postmortem samples drastically underestimated primate vocal capabilities. Our findings imply that the evolution of human speech capabilities required neural changes rather than modifications of vocal anatomy. Macaques have a speech-ready vocal tract but lack a speech-ready brain to control it.

Independent evidence from rocks, fossils, and genes converge on a cohesive narrative of isthmus formation in the Pliocene., The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas. To bring clarity to the question of when the Isthmus of Panama formed, we provide an exhaustive review and reanalysis of geological, paleontological, and molecular records. These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.