Automated species identification: why not?

Where possible, automation has been a common response of humankind to many activities that have to be repeated numerous times. The routine identification of specimens of previously described species has many of the characteristics of other activities that have been automated, and poses a major constraint on studies in many areas of both pure and applied biology. In this paper, we consider some of the reasons why automated species identification has not become widely employed, and whether it is a realistic option, addressing the notions that it is too difficult, too threatening, too different or too costly. Although recognizing that there are some very real technical obstacles yet to be overcome, we argue that progress in the development of automated species identification is extremely encouraging that such an approach has the potential to make a valuable contribution to reducing the burden of routine identifications. Vision and enterprise are perhaps more limiting at present than practical constraints on what might possibly be achieved.     

Endocytosis: why not wait to deubiquitinate?

Deubiquitination by the Fat facets protein - a regulator of photoreceptor differentiation during Drosophila eye development - has been found to activate endocytosis, while ubiquitination inhibits endocytosis. Surprisingly, this is the opposite effect that ubiquitination has on endocytosis of many plasma membrane proteins.     

Plant intelligence: Why,why not or where?

The concept of plant intelligence, as proposed by Anthony Trewavas, has raised considerable discussion. However, plant intelligence remains loosely defined; often it is either perceived as practically synonymous to Darwinian fitness, or reduced to a mere decorative metaphor. A more strict view can be taken, emphasizing necessary prerequisites such as memory and learning, which requires clarifying the definition of memory itself. To qualify as memories, traces of past events have to be not only stored, but also actively accessed. We propose a criterion for eliminating false candidates of possible plant intelligence phenomena in this stricter sense: an “intelligent” behavior must involve a component that can be approximated by a plausible algorithmic model involving recourse to stored information about past states of the individual or its environment. Re-evaluation of previously presented examples of plant intelligence shows that only some of them pass our test.

“You were hurt?” Kumiko said, looking at the scar.Sally looked down. “Yeah.”“Why didn''t you have it removed?”“Sometimes it''s good to remember.”“Being hurt?”“Being stupid.”—(W. Gibson: Mona Lisa Overdrive)

Key words: intelligence, memory, learning, plant development, mathematical models, plant neurobiology, definition of terms     

Folic acid fortification: why not vitamin B12 also?

Folic acid fortification of cereal grains was introduced in many countries to prevent neural tube defect occurrence. The metabolism of folic acid and vitamin B12 intersect during the transfer of the methyl group from 5-methyltetrahydrofolate to homocysteine catalyzed by B12-dependent methioine synthase. Regeneration of tetrahydrofolate via this reaction makes it available for synthesis of nucleotide precursors. Thus either folate or vitamin B12 deficiency can result in impaired cell division and anemia. Exposure to extra folic acid through fortification may be detrimental to those with vitamin B12 deficiency. Among participants of National Health And Nutrition Examination Survey with low vitamin B12 status, high serum folate (>59 nmol/L) was associated with higher prevalence of anemia and cognitive impairment when compared with normal serum folate. We also observed an increase in the plasma concentrations of total homocysteine and methylmalonic acid (MMA), two functional indicators of vitamin B12 status, with increase in plasma folate under low vitamin B12 status. These data strongly imply that high plasma folate is associated with the exacerbation of both the biochemical and clinical status of vitamin B12 deficiency. Hence any food fortification policy that includes folic acid should also include vitamin B12.     

Sound reasons for silence: why do molluscs not communicate acoustically?

Many adaptively beneficial states of form, behaviour and physiology are absent in large parts of the evolutionary tree of life. Although the causes of these absences can never be fully known, insights into the possibilities and limitations of adaptive evolution can be gained by examining the conditions that would be necessary for the forbidden phenotypes to evolve. Here, the case of acoustic communication in molluscs is considered. The production of sound as a warning to predators or as a means to attract mates is widespread among arthropods and vertebrates, both on land and in water, but is unknown among molluscs, even though many derived clades of gastropods and cephalopods are characterized by internal fertilization and by the evolution of long‐distance visual and chemical signalling. Many molluscs possess suitable hard parts – shell, operculum and jaws – for producing sound, but most shell‐bearing molluscs lack the agility or aggression necessary to cope with high‐activity enemies attracted to an acoustic beacon. Their evolutionary background, arising from the generally passive adaptations of molluscs and other animals with low metabolic rates, prevents selection favouring communication by sound, and indeed favours silence. Several clades of shell‐bearing gastropods and cephalopods were identified in which sound production has the greatest potential to arise or to be discovered. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 485–493.     

Are ecological systems chaotic - And if not, why not?

Chaotic dynamics emerge when positive/negative feedback systems are dominated much of the time by positive feedback growth processes. Although all ecological systems contain the seeds of chaos (positive feedback), empirical evidence and evolutionary/ecological reasoning support the view that ecosystems do not normally behave chaotically. They may, however, be driven to chaos by human actions that increase growth rates or induce delays in the regulatory (negative feedback) processes.     

Direct-to-consumer testing: if consumers are not anxious,why are policymakers?

Direct-to-consumer genetic testing continues to receive significant attention from both the popular press and policymakers. While the demand for these services has not, to date, been significant, it nevertheless seems likely that more and more individuals will be accessing DTC services. As a result, commentators have suggested that the DTC industry requires more oversight. A common rationale for policy action is that DTC services might cause undue anxiety. However, emerging evidence suggests that this is not the case. Indeed, it appears that genetic risk information has little impact on individual behavior or anxiety levels. Though more research is clearly needed, this type of research should inform the regulatory response to DTC services.     

Why be diurnal? Or, why not be cathemeral?

As a behavioural strategy, cathemerality is thought to confer considerable advantages by allowing animals to extend activity flexibly into either the diurnal or nocturnal phase in response to the prevailing ecological conditions. Factors such as temperature, access to food sources and minimising the risk of predation are all thought to be important in promoting cathemerality, although previous studies have produced inconsistent results. This paper adopts a different approach by first asking whether an obligate diurnal species, the chacma baboon (Papio hamadryas ursinus), exhibits seasonal variation in behavioural flexibility in response to annual cycles of day length. While short day lengths are an important constraint on the activity of the baboons at De Hoop Nature Reserve, South Africa, long summer days permit considerable flexibility in thermoregulatory response, diet selection and patterns of habitat choice. Given that baboons adapt flexibly in response to a relaxation of time constraints, the question thus arises as to why diurnal and nocturnal primates do not adopt cathemeral activity patterns when time is constrained? For baboons, the costs of predation appear to prohibit exploitation of the nocturnal phase and it is likely that such constraints are true of most primates. It thus follows that Madagascar's predatory environment must in some way permit or select for a cathemeral lifestyle. The importance of the predation by fossa (Cryptoprocta ferox) on the evolution of cathemerality is discussed.     

Residual linkage: why do linkage peaks not disappear after an association study?

Family-based candidate gene and genome-wide association studies are a logical progression from linkage studies for the identification of gene and polymorphisms underlying complex traits. An efficient way to analyse phenotypic and genotypic data is to model linkage and association simultaneously. An important result from such an analysis is whether any evidence for linkage remains after fitting polymorphisms at candidate genes (residual linkage), because this may indicate locus and allelic heterogeneity in the population and will influence subsequent molecular strategies. Here we report that substantial residual linkage is to be expected, even under genetic homogeneity and when the underlying causal polymorphisms are genotyped and fitted in the model. We simulated a powerful design to detect linkage to quantitative trait loci, with 5, 10 or 20 causal SNPs spread throughout the genome. These SNPs were responsible for all genetic variation, and hence for both linkage and association. Residual linkage at the largest linkage peak from a genome-wide scan was substantial, with mean LOD scores of 0.4, 0.7, and 1.4 for the case of 5, 10 and 20 underlying causal SNPs, respectively. For less powerful designs, the proportion of the original LOD scores that remains after association will be even larger. All cases of ‘significant’ residual linkage are false positives. The reason for the apparent paradox of detecting residual linkage after fitting causal polymorphisms is that the linkage signals at the largest peaks in a genome-scan are severely inflated, even if all peaks correspond to true linkage. Our findings are general and apply to linkage mapping of any phenotype and to any pedigree structure.     

Autism: not interested or not 'tuned-in'?

Recent studies of perceptual adaptation to faces have revolutionised our understanding of neural mechanisms that support face recognition. A new study has applied this approach to autistic spectrum disorders, revealing severe deficits in such adaptation.