Science Driven Restoration: A Candle in a Demon Haunted World—Response to Cabin (2007)

Cabin (2007) asks whether formal science is an effective framework and methodology for designing and implementing ecological restoration programs. He argues that beyond certain ancillary benefits, restoration science has little of practical value to offer the practice of restoration. He goes on to suggest that restoration science most often represents an impediment to restoration practice because an “ivory tower” mentality limits the utility of experiments and diverts research dollars away from answering practical questions. His conclusion is that a nonscientific gardening approach may be more effective at restoring degraded ecosystems. We disagree with this perspective because: (1) restoration science has moved beyond exclusively using “square grids” placed on small patches of land to examine treatment effects on species representation; (2) Cabin’s critique greatly undervalues the contribution of science to restoration practice even where the input of restoration scientists is not directly evident; and (3) the practice of restoration is unlikely to advance beyond small‐scale and truly haphazard successes without well‐designed studies that can provide peer‐reviewed and widely accessible published information on the mechanisms underlying both successes and failures. We conclude that through integration with other disciplines, restoration science increasingly will provide novel approaches and tools needed to restore ecosystem composition, structure, and function at stand to landscape scales. As with the broader role of science in the human enterprise ( Sagan 1996 ), the contribution of restoration science to restoration practice can only grow as the discipline matures.     

No Evidence‐Based Restoration Without a Sound Evidence Base: A Reply to Guldemond et al.

Evidence‐based practice is not possible without an evidence base. Guldemond et al. confuse our attempt at assessing the status of the evidence base of restoration programs in South Africa with attempting to assess whether restoration is evidence‐based. While we fully agree with them that there is a need to assess whether practitioners use evidence in their decision‐making, we assert that use of evidence is the last step in the evidence‐based approach. It is preceded by the generation (and documentation) of evidence through baseline condition assessment, proper goal setting, sound monitoring of the impacts of the chosen intervention as well as effective dissemination of resulting evidence. To answer the question whether restoration is evidence‐based would require the assessment of all stages from generation to use. We chose to start at the beginning, a logical place to start.     

The SER Standards: a globally relevant and inclusive tool for improving restoration practice—a reply to Higgs et al.

In response to a critique by Higgs et al., this article clarifies the content and intent of the Society for Ecological Restoration's (SER) International Standards for the Practice of Ecological Restoration. Higgs et al. expressed concern that the SER Standards are not sufficiently underpinned by principles and risk disenfranchising some practitioners by narrowing what qualifies as ecological restoration. To demonstrate that these concerns are unfounded, we discuss the policy context and principles on which the Standards are based, its organizational structure, the innovative and inclusive approach used for development, and highlight significant errata by Higgs et al.     

Applied nucleation is a straightforward,cost‐effective forest restoration approach: reply to Ramírez‐Soto et al. (2018)

We agree with Ramírez‐Soto and colleagues that applied nucleation can be an effective approach for tropical forest restoration both in lowland and higher elevation tropical forests. We also contend that it is cheaper than standard plantation‐style plantings and is straightforward to train personnel to implement this approach.     

Theorizing human impacts into ecological restoration is not a slippery slope,but a toehold for reaching social‐ecological resilience: a counter‐response to McDonald et al. (2019)

In their reply, McDonald et al. have misconstrued several crucial points from our article. In this counter‐response, we clarify our concerns with the Standards as a document with global implications. We highlight our concern with framing preindustrial indigenous peoples' impacts as natural and the colonial connotations of such an assumption. We also discuss practical issues that arise from the Standards' conceptualization of natural variation and suggest avenues for developing frameworks that do not rely on a nature‐culture dichotomy or naturalization of indigenous landscapes.     

Open science and meta‐analysis allow for rapid advances in ecology: A response to Menegotto et al. (2019)

Menegotto and colleagues’ (2019) commentary on our paper (Kinlock et al., 2018) does not negate our findings, but by recategorizing and reanalysing a portion of our data set, advances our knowledge of the latitudinal diversity gradients (LDGs) in marine ecosystems, particularly emphasizing different findings for benthic LDGs as a result of the recategorization of the data. Furthermore, we see the contribution by Menegotto et al. (2019) as highlighting the importance of scientific transparency; we believe that this insight into the nature of LDGs in marine systems would have been delayed, if not unobtainable, had we not provided fully transparent methods and complete data in our paper.     

The power of potential natural vegetation (and of spatial‐temporal scale): a response to Carrión & Fernández (2009)

A commentary by Carrión & Fernández (Journal of Biogeography, 2009, 36 , 2202–2203) compared Holocene pollen records with models of potential natural vegetation (PNV) proposed in the phytosociological literature and concluded that the predicted PNV resulted from anthropogenic disturbance. However, the authors misinterpreted PNV, leading to two serious flaws in their assumptions: (1) PNV is not defined as a pre‐anthropic or climax plant community; and (2) PNV is not a concept restricted to the phytosociological method. Therefore we criticize the conclusions expressed in the commentary, and we stress the need for an interdisciplinary approach based on multi‐temporal and multi‐spatial scales to achieve a modern framework for the study of plant communities.     

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145

Background  

Yu et al. (BMC Bioinformatics 2007,8: 145+) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nucleotide polymorphism arrays. One of the methods compared is our non-homogenous Hidden Markov Model approach. Our approach uses Markov Chain Monte Carlo for inference, but Yu et al. ran the sampler for a severely insufficient number of iterations for a Markov Chain Monte Carlo-based method. Moreover, they did not use the appropriate reference level for the non-altered state.     

An annotated list of species of the Proteocephalus Weinland, 1858 aggregate sensu de Chambrier et al. (2004) (Cestoda: Proteocephalidea), parasites of fishes in the Palaearctic Region, their phylogenetic relationships and a key to their identification

A list and key to the identification of valid species of tapeworms of the Proteocephalus Weinland, 1858 aggregate sensu de Chambrier et al. (2004), i.e. species of the genus occurring in fresh- and brackish-water fishes in the Palaearctic Region, are provided, with data on their hosts and geographical distribution. Instead of 32 taxa listed by Schmidt (1986) and subsequent authors, only the following 14 species are considered to be valid: P. ambiguus (Dujardin, 1845) (type-species); P. cernuae (Gmelin, 1790); P. filicollis (Rudolphi, 1802); P. fluviatilis Bangham, 1925; P. gobiorum Dogiel & Bychowsky, 1939; P. longicollis (Zeder, 1800); P. macrocephalus (Creplin, 1825); P. midoriensis Shimazu, 1990; P. percae (Müller, 1780); P. plecoglossi Yamaguti, 1934; P. sagittus (Grimm, 1872); P. tetrastomus (Rudolphi, 1810); P. thymalli (Annenkova-Chlopina, 1923); and P. torulosus (Batsch, 1786). An analysis of sequences of the nuclear genes (ITS2 and V4 region of 18S rDNA) revealed the following phylogenetic relationships for these taxa: P. torulosus ((P. midoriensis, P. sagittus) (P. fluviatilis (P. filicollis, P. gobiorum, P. macrocephalus)) (P. cernuae, P. plecoglossi, P. tetrastomus ((P. longicollis, P. percae) (P. ambiguus, P. thymalli)))). P. pronini Rusinek, 2001 from grayling Thymallus arcticus nigrescens is synonymised with P. thymalli. P. esocis La Rue, 1911 is apparently invalid but its conspecificity with either P. percae or P. longicollis could not be confirmed due to the absence of the scolex in the holotype and the unavailability of other material for morphological and molecular studies. P. osculatus (Goeze, 1782) has recently been transferred to Glanitaenia de Chambrier, Mariaux, Vaucher & Zehnder, 2004. The validity of the genus is supported by the position of G. osculata within the Proteocephalidea, based on molecular data, as well as its morphology and nature of the definitive host (the European wels Silurus glanis). P. hemispherous Rahemo & Al-Niaeemi, 2001, described from S. glanis in Iraq, is transferred to Postgangesia Akhmerov, 1960 as Postgangesia hemispherous (Rahemo & Al-Niaeemi, 2001) n. comb.     

“Earliest Zanclean age for the Colombacci and uppermost Di Tetto formations of the « latest Messinian » northern Apennines: New palaeoenvironmental data from the Maccarone section (Marche Province, Italy)” by Popescu et al. (2007) Geobios 40 (359-373)

Two possible alternative interpretations of the claimed Zanclean age (Popescu et al., 2007) of two historical lithostratigraphic units of the Northern Apennines, usually referred to as Late Messinian in age and recording the so called Lagomare final event of the Messinian salinity crisis (MSC), are here discussed. The wrong age attribution of the Colombacci and “tetto” Fms. is ruled out based on data from the Maccarone and other sections showing that the Colombacci-Argille Azzurre Fm. boundary is basin wide synchronous and coincident with the Miocene-Pliocene boundary as far as it has been formally defined in the Eraclea Minoa GSSP. Alternatively, the opportunity of emending the Zanclean GSSP to a stratigraphically lower horizon recording the first evidence of marine influences in the Mediterranean following the MSC peak, seems not suitable, as (1) the marine signature of uppermost Messinian deposits is weak and still controversial and (2) no significant bio- and magnetostratigraphic events, well chronologically defined and recognizable at a global scale appear to be available to such a purpose.     

Lipoprotein(a) and Atherosclerotic Cardiovascular Disease,the Impact of Available Lipid-Lowering Medications on Lipoprotein(a): An Update on New Therapies

ObjectiveTo review evidence of existing and new pharmacological therapies for lowering lipoprotein(a) (Lp[a]) concentrations and their impact on clinically relevant outcomes.MethodsWe searched for literature pertaining to Lp(a) and pharmacological treatments in PubMed. We reviewed articles published between 1963 and 2020.ResultsWe found that statins significantly increased Lp(a) concentrations. Therapies that demonstrated varying degrees of Lp(a) reduction included ezetimibe, niacin, proprotein convertase subtilisin/kexin type 9 inhibitors, lipoprotein apheresis, fibrates, aspirin, hormone replacement therapy, antisense oligonucleotide therapy, and small interfering RNA therapy. There was limited data from large observational studies and post hoc analyses showing the potential benefits of these therapies in improving cardiovascular outcomes.ConclusionThere are multiple lipid-lowering agents currently being used to treat hyperlipidemia that also have a Lp(a)-lowering effect. Two RNA therapies specifically targeted to lower Lp(a) are being investigated in phase 3 clinical trials and, thus far, have shown promising results. However, evidence is lacking to determine the clinical relevance of reducing Lp(a). At present, there is a need for large-scale, randomized, controlled trials to evaluate cardiovascular outcomes associated with lowering Lp(a).