Site of graviperception in roots: a re-examination

Two lines of evidence have been cited to support the assertion that the root cap is the sole site of graviperception in the root. The first evidence is based on surgical removal of the cap, which abolishes the response to gravity. This is sufficient to conclude that the cap is involved in gravitropism, but not to conclude that the cap is the site of graviperception. The second is based on the results of centrifugation experiments, in which different parts of the plant are subjected to different centrifugal forces. The data from such experiments have been cited to support the conclusion that the perception of gravity is limited to the rootcap. However, these data actually support the conclusion that gravity is perceived throughout the root tip, and not only in the root cap. We believe that the data support the conclusion that the root cap is involved in root gravitropism, but that there is inadequate evidence to conclude that the cap is the sole site of graviperception.     

Rationality, biology and optimality*

A historical theory of rational norms claims that, if we are supposed to think rationally, this is because it is biologically normal for us to do so. The historical theorist is committed to the view that we are supposed to think rationally only if, in the past, adult humans sometimes thought rationally. I consider whether there is any plausible model of rational norms that can be adopted by the historical theorist that is compatible with the claim that adult human beings are subject to rational norms, given certain plausible empirical assumptions about our history and capabilities. I suggest that there is one such model: this model centres on the idea that a procedure is rational if it has been endorsed (or at least not rejected) by mechanisms that have the function to ensure that the subject learns to reason in a way that approaches a certain kind of optimality. This revised version was published online in July 2006 with corrections to the Cover Date.     

Modelling Thrombin Generation in Human Ovarian Follicular Fluid

A mathematical model is constructed to study thrombin production in human ovarian follicular fluid. The model results show that the amount of thrombin that can be produced in ovarian follicular fluid is much lower than that in blood plasma, failing to reach the level required for fibrin formation, and thereby supporting the hypothesis that in follicular fluid thrombin functions to initiate cellular activities via intracellular signalling receptors. It is also concluded that the absence of the amplification pathway to thrombin production in follicular fluid is a major factor in restricting the amount of thrombin that can be produced. Titration of the initial concentrations of the various reactants in the model lead to predictions for the amount of tissue factor and phospholipid that is required to maintain thrombin production in the follicle, as well as to the conclusion that tissue factor pathway inhibitor has little effect on the time that thrombin generation is sustained. Numerical experiments to determine the effect of factor V, which is at a much reduced level in follicular fluid compared to plasma, and thrombomodulin, illustrate the importance for further experimental work to determine values for several parameters that have yet to be reported in the literature.     

Cancer Development and Progression: A Non-Adaptive Process Driven by Genetic Drift

The current mainstream in cancer research favours the idea that malignant tumour initiation is the result of a genetic mutation. Tumour development and progression is then explained as a sort of micro-evolutionary process, whereby an initial genetic alteration leads to abnormal proliferation of a single cell that leads to a population of clonally derived cells. It is widely claimed that tumour progression is driven by natural selection, based on the assumption that the initial tumour cells acquire some properties that endow such cells with a selective advantage over the normal cells from which the tumour cells are derived. The standard view assumes that the transformed bodily cell somehow acquires "responsiveness" to natural selection independently of the whole organism to which the cell belongs. Yet, it is never explained where such an acquired capacity to respond to natural selection by the individual bodily cell comes from. This situation poses many difficult questions that so far have been left unanswered. For example, there is no explanation why some cells belonging to an organised whole and as such having no independent capacity for survival, apparently become 'independent' entities, able to respond to selective pressures in an autonomous fashion and then to be evaluated by natural selection. Hereunder it is argued that such a qualitative change cannot be the consequence of specific genetic mutations. Moreover, it is shown that natural selection is unlikely to be acting within the organism during tumour development and progression and that tumour evolution is a random, non-adaptive process, driven by no fundamental biological principle. Thus, mutations in the so-called oncogenes and tumour suppressor genes observed in epithelial cancers (that constitute more than 90% of all cancers) are not the result of selection for better cellular growth or survival under restrictive conditions. Instead, here it is suggested that they are the consequence of genetic drift acting upon gene functions that become non-relevant, either for the individual or the species fitness, once the organism is past its reproductive prime and as such, they also become superfluous for cell survival in the short term. It is proposed that the origin of cancer is epigenetic and it is a consequence of the need for a continued turnover of the individuals that constitute a species.     

CONSPIRATORIAL WHISPERS AND CONSPICUOUS DISPLAYS: GAMES OF SIGNAL DETECTION

Recent models of signaling have assumed that the expenditure required to ensure detection of a display is negligible and have concentrated instead on the costs that may be necessary to maintain honesty. Such models predict that individuals who share the same interests are likely to communicate using “conspiratorial whispers,” signals that are cheap and inconspicuous. Here, I present a game-theoretical model of signal detection (in a noisy environment, in the presence of potential eavesdroppers), which demonstrates that the idea of conspiratorial whispers is far too simplistic. It is true that in “cooperative” signaling systems (where signalers attempt to elicit responses that are beneficial for receivers), signal cost is not required to maintain honesty. However, some level of expenditure is still needed to ensure that a signal is reliably detected. Moreover, there exists a conflict of interest between signalers and receivers over the division of this expenditure. To predict the stable level of display in such cases, one needs to know how this conflict of interest will be resolved. The model reveals that the outcome may range from a whisper to a conspicuous and costly (though still conspiratorial) display. The more closely related the receiver is to the signaler, the greater the level of signal exaggeration that is expected—the opposite prediction to that of honest signaling models.     

Janus-faced race: Is race biological,social, or mythical?

As belief in the reality of race as a biological category among U.S. anthropologists has fallen, belief in the reality of race as a social category has risen in its place. The view that race simply does not exist—that it is a myth—is treated with suspicion. While racial classification is linked to many of the worst evils of recent history, it is now widely believed to be necessary to fight back against racism. In this article, I argue that race is indeed a biological fiction, but I critique the claim that race is socially real. I defend a form of anti-realist reconstructionism about race, which says that there are no races, only racialized groups—groups mistakenly believed to be races. I argue that this is the most attractive position about race from a metaphysical perspective, and that it is also the position most conductive to public understanding and social justice.     

What is this stuff called fitness?

This paper considers a variety of attempts to define fitness in such a way as to defend the theory of evolution by natural selection from the criticism that it is a circular argument. Each of the definitions is shown to be inconsistent with the others. The paper argues that the environment in which an animal evolves can be defined only with respect to the properties of the phenotype of the animal and that it is therefore not illuminating to try to explain the phenotypic properties of the animal in terms of adaptation to an environment that is defined by those very properties. Furthermore, since there is no way that the environment can be defined independently of the presence of the animal there is no way that the quality of an animal can be assessed; and there can be no objective criteria by whichany form of selection can be carried out, therefore there can be no criteria by whichnatural selection can be carried out. It is proposed that fitness is nothing more than the production of offspring, that this is a phenotypic property like all the others, and if it is heritable then the offspring of the parents that produce the most offspring will themselves produce the most offspring, and that in principle it is impossible to account for this in terms of the other phenotypic properties of the fittest animals except by circular argument. Differential rates of reproduction are the causes of evolution and the phenotypic causes are strictly inexplicable.     

ENHANCING EVOLUTION AND ENHANCING EVOLUTION

It has been claimed in several places that the new genetic technologies allow humanity to achieve in a generation or two what might take natural selection hundreds of millennia in respect of the elimination of certain diseases and an increase in traits such as intelligence. More radically, it has been suggested that those same technologies could be used to instil characteristics that we might reasonably expect never to appear due to natural selection alone. John Harris, a proponent of this genomic optimism, claims in his book Enhancing Evolution that we not only have it in our power to enhance evolution, but that we also have a duty to do so. In this paper, I claim that Harris' hand is strong but that he overplays it nevertheless. He is correct to dismiss the arguments of the anti‐enhancement lobby and correct to say that enhancement is permissible; but ‘good’ is different from ‘permissible’ and his argument for the goodness of enhancement is less convincing. Moreover, he is simply wrong to claim that it generates a duty to enhance.     

Do grasslands act as a perpetual sink for carbon?

It is increasingly commonly suggested that grasslands are a perpetual sink for carbon, and that just maintaining grasslands will yield a net carbon sink. I examine the evidence for this from repeated soil surveys, long term grassland experiments and simple mass balance calculations. I conclude that it is untenable that grasslands act as a perpetual carbon sink, and the most likely explanation for observed grassland carbon sinks over short periods is legacy effects of land use and land management prior to the beginning of flux measurement periods. Simply having grassland does not result is a carbon sink, but judicious management or previously poorly managed grasslands can increase the sink capacity. Given that grasslands are a large store of carbon, and that it is easier and faster for soils to lose carbon that it is for them to gain carbon, it is an important management target to maintain these stocks.     

CSF-1 and TPA stimulate independent pathways leading to lysosomal degradation or regulated intramembrane proteolysis of the CSF-1 receptor

The CSF-1 receptor is a protein-tyrosine kinase that has been shown to undergo regulated intramembrane proteolysis, or RIPping. Here, we have compared receptor downregulation and RIPping in response to CSF-1 and TPA. Our studies show that CSF-1 is a relatively poor inducer of RIPping and that CSF-1-induced receptor downregulation is largely independent of RIPping. TPA is a strong inducer of RIPping and TPA-induced receptor downregulation is mediated by RIPping. We further found that RIPping is dependent on TACE or a TACE-like protease, that CSF-1 and TPA use independent pathways to initiate RIPping, and that the intracellular domain is targeted for degradation through ubiquitination.     

CHEAP LISTENING? – REFLECTIONS ON THE CONCEPT OF WRONGFUL DISABILITY1

This paper investigates the concept of wrongful disability. That concept suggests that parents are morally obligated to prevent the genetic transmission of certain conditions and so, if they do not, any resulting disability is 'wrongful'. In their book From Chance to Choice, Buchanan, Brock, Daniels and Wikler defend the concept of wrongful disability using the principle of avoidability via substitution. That principle is scrutinised here. It is argued that the idea of avoidability via substitution is both conceptually problematic and rather insensitive. Instead, it is suggested that the question of whether or not bringing a particular disability about is wrongful does not simply hinge on whether or not substitution takes place. Rather, it involves an evaluation of parental aspirations and responsibilities. It is argued that the desire need not be responsible for creating challenges for others that lie outside what is perceived to be an acceptable range provides a justification for termination of pregnancy on the grounds of projected disability that neither commits one to wrongful life claim, nor requires that one substitute a non-disabled child instead. The ramifications of such an approach are explored. The paper concludes by suggesting that the question of what is considered to be an acceptable range of human capability is an increasingly important one. It is argued that, when addressing that question, we should be acutely aware of the social context that may go some way to define what we consider to be an acceptable range.     

An engram found? Evaluating the evidence from fruit flies

Is it possible to localize a memory trace to a subset of cells in the brain? If so, it should be possible to show: first, that neuronal plasticity occurs in these cells. Second, that neuronal plasticity in these cells is sufficient for memory. Third, that neuronal plasticity in these cells is necessary for memory. Fourth, that memory is abolished if these cells cannot provide output during testing. And fifth, that memory is abolished if these cells cannot receive input during training. With regard to olfactory learning in flies, we argue that the notion of the olfactory memory trace being localized to the Kenyon cells of the mushroom bodies is a reasonable working hypothesis.     

John Harris' argument for a duty to research

John Harris suggests that partcipation in or support research, particularly medical research, is a moral duty. One kind of defence of this position rests on an appeal to the past, and produces two arguments. The first of these arguments is that it is unfair to accept the benefits of research without contributing something back in the form of support for, or participation in, research. A second argument is that we have a social duty to maintain those practices and institutions that sustain us, such as those which contribute to medical knowledge. This argument is related to the first, but it does not rely so heavily on fairness. Another kind of defence of the duty to research rests on an appeal to the future benefits of research: research is an effective way to discharge a duty to rescue others from serious illness or death, therefore we have a duty to research. I suggest that all three of Harris' lines fail to provide a compelling duty to research and spell out why. Moreover, not only do the lines of argument fail in their own terms: in combination, they turn out to be antagonistic to the very position that Harris wants to defend. While it is not my intention here to deny that there might be a duty to research, I claim that Harris' argument for the existence of such a duty is not the best way to establish it.     

The interpretation of habitat preference metrics under use�Cavailability designs

Models of habitat preference are widely used to quantify animal–habitat relationships, to describe and predict differential space use by animals, and to identify habitat that is important to an animal (i.e. that is assumed to influence fitness). Quantifying habitat preference involves the statistical comparison of samples of habitat use and availability. Preference is therefore contingent upon both of these samples. The inferences that can be made from use versus availability designs are influenced by subjectivity in defining what is available to the animal, the problem of quantifying the accessibility of available resources and the framework in which preference is modelled. Here, we describe these issues, document the conditional nature of preference and establish the limits of inferences that can be drawn from these analyses. We argue that preference is not interpretable as reflecting the intrinsic behavioural motivations of the animal, that estimates of preference are not directly comparable among different samples of availability and that preference is not necessarily correlated with the value of habitat to the animal. We also suggest that preference is context-dependent and that functional responses in preference resulting from changing availability are expected. We conclude by describing advances in analytical methods that begin to resolve these issues.     

Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein

Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) that converts pyruvate and coenzyme A into acetyl-CoA and formate in a reaction that is crucial to the primary metabolism of many anaerobic bacteria. The glycyl radical cofactor, which is posttranslationally installed by a radical S-adenosyl-L-methionine (SAM) activase, is a simple and effective catalyst, but is also susceptible to oxidative damage in microaerobic environments. Such damage occurs at the glycyl radical cofactor, resulting in cleaved PFL (cPFL). Bacteria have evolved a spare part protein termed YfiD that can be used to repair cPFL. Previously, we obtained a structure of YfiD by NMR spectroscopy and found that the N-terminus of YfiD was disordered and that the C-terminus of YfiD duplicates the structure of the C-terminus of PFL, including a β-strand that is not removed by the oxygen-induced cleavage. We also showed that cPFL is highly susceptible to proteolysis, suggesting that YfiD rescue of cPFL competes with protein degradation. Here, we probe the mechanism by which YfiD can bind and restore activity to cPFL through enzymatic and spectroscopic studies. Our data show that the disordered N-terminal region of YfiD is important for YfiD glycyl radical installation but not for catalysis, and that the duplicate β-strand does not need to be cleaved from cPFL for YfiD to bind. In fact, truncation of this PFL region prevents YfiD rescue. Collectively our data suggest the molecular mechanisms by which YfiD activation is precluded both when PFL is not damaged and when it is highly damaged.     

Execution by lethal injection, euthanasia, organ-donation and the proper goals of medicine

In a recent issue of this journal, David Silver and Gerald Dworkin discuss the physicians' role in execution by lethal injection. Dworkin concludes that discussion by stating that, at that point, he is unable to think of an acceptable set of moral principles to support the view that it is illegitimate for physicians to participate in execution by lethal injection that would not rule out certain other plausible moral judgements, namely that euthanasia is under certain conditions legitimate and that organ-donation surgery is sometimes permissible. This article draws attention to some problems in the views of Silver and Dworkin and suggests moral principles which support the three moral views just mentioned.     

Predictive glycoengineering of biosimilars using a Markov chain glycosylation model

Biosimilar drugs must closely resemble the pharmacological attributes of innovator products to ensure safety and efficacy to obtain regulatory approval. Glycosylation is one critical quality attribute that must be matched, but it is inherently difficult to control due to the complexity of its biogenesis. This usually implies that costly and time‐consuming experimentation is required for clone identification and optimization of biosimilar glycosylation. Here, a computational method that utilizes a Markov model of glycosylation to predict optimal glycoengineering strategies to obtain a specific glycosylation profile with desired properties is described. The approach uses a genetic algorithm to find the required quantities to perturb glycosylation reaction rates that lead to the best possible match with a given glycosylation profile. Furthermore, the approach can be used to identify cell lines and clones that will require minimal intervention while achieving a glycoprofile that is most similar to the desired profile. Thus, this approach can facilitate biosimilar design by providing computational glycoengineering guidelines that can be generated with a minimal time and cost.     

Risk avoidance and nesting strategies

Gillespie (1974,1975) has shown that selection will tend to minimize variance in offspring number. It is shown that this effect is due to selection maximizing the average number of surviving offspring when there is density-dependent survival, and that it is unnecessary to invoke principles such as minimizing the variability of fitness (Real, 1980). The effect of this principle of selecting for laying several small clutches rather than one large clutch when there is predation on whole clutches is investigated. It is found that the selection pressure is weak, contrary to the conclusion of Rubenstein (1982), and is unlikely to be of evolutionary importance.     

Why the embryo rescue case is a bad argument against embryonic personhood

The embryo rescue case (ERC) is a thought experiment that is used to argue against the view that embryos have a right to life (i.e., are persons). I will argue that cognitive science undermines the intuition elicited by the ERC. I will show that whether or not embryos have a right to life, our mental tools will make it very difficult to believe that they do have the said right. This suggests that the intuition elicited by the ERC is not truth‐indicative. The upshot of this is that we have an undercutting defeater for our intuition that embryos do not have a right to life. Thus, the ERC is a bad argument against embryonic personhood.