Adaptation and gain normalization: a comment on Ullman & Schechtman (1982)

A well-known process for adaptation and gain normalization is compared with the process described by S. Ullman and G. Schechtman (Proc. R. Soc. Lond. B 216, 299-313 (1982)). A neural interpretation of this process in terms of transmitter gating, slow accumulation, and release is described. Applications to a wide variety of problems in perception, cognition, and motivated behaviour can be made by embedding the gating process into opponent processes, notably shunting on-centre off-surround networks, to form a network module called a gated dipole field.     

The value of repetitive sequences in chloroplast DNA for phylogeographic inference: a comment on Vachon & Freeland 2011

In a recent Technical Advance article, Vachon and Freeland (2011, Molecular Ecology Resources, 11, 279-285.) evaluate the utility of repetitive and non-repetitive variation in the chloroplast genome for phylogeographic inference, using variation in Phragmites australis as an example. While we agree that repetitive and nonrepetitive regions evolve at different rates and homoplasy can impact results, we disagree with the conclusion that repetitive regions are inappropriate for large-scale phylogeographic studies. Here we describe limitations to the study dataset and analysis, and provide an alternative viewpoint on the utility of repetitive regions for phylogeographic studies.     

The biophysical properties of spines as a basis for their electrical function: a comment on Kawato & Tsukahara (1983)

In a theoretical study of the passive cable properties of dendritic spines Kawato & Tsukahara (1983) claim to have proved that "the dendritic spine has no significant electrical function" (from their discussion). However, Kawato & Tsukahara restrict their analysis to current inputs to spines. Since the dimensions of spines are very small, their input resistance is expected to be very large and the synaptic input to spines has to be modeled as conductance change. Under this assumption, spines show interesting (non-linear) electrical properties: i) the somatic potential induced by an excitatory synapse on a spine may depend strongly on the shape of the spine and ii) the effect of inhibition might be confined to the spine.     

Shifting base-lines, declining coral cover, and the erosion of reef resilience: comment on Sweatman et al. (2011)

Formal monitoring of the Great Barrier Reef was initiated in 1986 in response to the clear scientific evidence (and growing public concern) over the loss of corals caused by two protracted outbreaks of crown-of thorns starfish, which began in 1962 and 1979. Using monitoring data from manta tows along and across the Great Barrier Reef, Sweatman et al. (Coral Reefs 30:521–531, 2011) show that coral cover after these outbreaks declined further from 28 to 22% between 1986 and 2004. Pointing to the current levels of protection of the Great Barrier Reef, they state that earlier estimates of losses of coral cover since the early 1960s have been exaggerated. However, the loss of close to one-quarter of the coral cover over the past two decades represents an average loss of 0.34% cover per year across the whole GBR after 1986, which is very similar to previously reported rates of annual loss measured over a longer timeframe. The heaviest recent losses have occurred on inshore and mid-shelf reefs, which Sweatman et al. (Coral Reefs 30:521–531, 2011) attribute to a natural cycle of disturbance and recovery. But there has been very limited recovery. While coral cover has increased for short periods on some individual reefs, it has declined sharply on many more to produce the observed system-wide trend of declining cover. Close to 40% of coral cover on inner reefs has been lost since 1986. Of particular significance is the new evidence that coral cover has remained unchanged or declined further from a low 1986 baseline in 28 out of 29 sub-regions of the Great Barrier Reef, indicating a gradual erosion of resilience that is impeding the capacity of this huge reef system to return towards its earlier condition. This result, and other clear evidence of widespread incremental degradation from overfishing, pollution, and climate change, calls for action rather than complacency or denial.     

Rethinking the relationship between nestedness and beta diversity: a comment on Baselga (2010)

Baselga [Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19 , 134–143, 2010] proposed pairwise (β_nes) and multiple‐site (β_NES) beta‐diversity measures to account for the nestedness component of beta diversity. We used empirical, randomly created and idealized matrices to show that both measures are only partially related to nestedness and do not fit certain fundamental requirements for consideration as true nestedness‐resultant dissimilarity measures. Both β_nes and β_NES are influenced by matrix size and fill, and increase or decrease even when nestedness remains constant. Additionally, we demonstrate that β_NES can yield high values even for matrices with no nestedness. We conclude that β_nes and β_NES are not true measures of the nestedness‐resultant dissimilarity between sites. Actually, they quantify how differences in species richness that are not due to species replacement contribute to patterns of beta diversity. Finally, because nestedness is a special case of dissimilarity in species composition due to ordered species loss (or gain), the extent to which differences in species composition is due to nestedness can be measured through an index of nestedness.     

Further comment on the coccidian nature of cryptosporidia (Sporozoa: Apicomplexa)

The coccidian nature of the genus Cryptosporidium was undoubtedly accepted by Tyzzer who was the first to describe this sporozoan parasite in 1907. Electron microscopic studies made in 70-90s demonstrated the intracellular, although extracytoplasmic localization of Cryptosporidium spp. The pattern of Cryptosporidium life cycle fits well that of other intestinal homogeneous coccidian genera of the suborder Eimeriina: macro- and microgamonts develop independently, a microgamont gives rise to numerous male gametes, oocysts serving for parasite's spreading in the environment. Along with these characters, Cryptosporidium spp. demonstrate some secondary peculiarities (an endogenous phase of development in microvilli of epithelial surfaces, two morphofunctional types of oocysts, the smallest number of sporozoites per oocyst, a multi-membraneous "feeder" organelle etc.), which may be due presumably to their early acquisition of specialization in the course of evolution. The recent studies based on molecular sequence data (18S rRNA) applied to 8 eimeriid and isosporid coccidian genera (Morrison, Ellis, 1997), suggested that the subclass Coccidia (class, according to Morrison and Ellis) be considered monophylic if Cryptosporidium were excluded, and this genus was regarded as the sister group to the rest of the Apicomplexa, or as the sister to the suborder (class) Hematozoa within the Apicomplexa. Either of these placements of Cryptosporidium definitely conflicts with both the generally accepted taxonomic scheme by Levine (1982) and the phenotypically based phylogeny of the phylum Apicomplexa (Barta e. a., 1990). The author's opinion is that the differences between the examined eimeriid and isosporid coccidia, on the one hand, and Cryptosporidium, on the other hand, provided by molecular sequence data, may testify primarily to the well known morphofunctional dissimilarities between the compared organisms, rather than cast doubt on the coccidian nature of Cryptosporidium. Again, these data can hardly prove that Cryptosporidium does not belong to the coccidia. Thus, the modern molecular sequence data, despite their obvious scientific value, would make sense for phylogeny estimation only, if they are critically analysed and considered in combination with results of the relevant basic research.