Engelhardt's Diagnosis and Prescription: Persuasive or Problematic?

In a spirit of critical appreciation, this essay challenges several core aspects of the critique of secular morality and the defense of Orthodox Christianity offered by H. Tristram Engelhardt in After God. First, I argue that his procedurally driven approach to a binding morality based solely on a principle of permission leaves morality without any substantive definition in general terms, in ways that are both conceptually problematic and also at odds with Engelhardt's long-standing distinction between non-malevolence and beneficence. Second, I question the accuracy or adequacy of Engelhardt's critique of the Enlightenment project for his unwarranted privileging of a particular version of Enlightenment thinking at the expense of other Enlightenment perspectives less amenable to Engelhardt's working generalizations. Third, I challenge the theoretical cogency of Engelhardt's insistence on the ubiquity and intractability of moral controversies and his depiction of moral strangers and moral friends as, in effect, mutually exclusive terms. Finally, I question Engelhardt's embrace of a divine command model of ethics as the appropriate resolution of Euthyphro's dilemma and suggest that there may be intermediate approaches to the usual starkly drawn contrasts between divine command and naturalist accounts.

Effects of nitrogen on caesium allocation in rice plants (Oryza sativa).

After the nuclear accident in Fukushima Prefecture, Japan, in 2011, 137 Caesium (Cs) contaminated nearby agricultural regions. Studies in these rice fields found that low K and high N fertilizer application enhanced Cs uptake in rice shoots. However, the influence of root and soil physics on these findings, as well as precise nutrient levels, remain to be clarified. We sought to analyse these relationships utilizing hydroponically grown rice plants. The rice plants were subjected to various concentrations of K and N nutrient solutions. We measured Cs allocation within the plants and performed transcript analyses using root tissues. Under low-K conditions, low-N plants accumulated less Cs in shoots and more in roots when compared to control-N conditions, even though overall Cs uptake remained unchanged. Expression analyses of root mRNAs showed that low-N plants accumulated reduced levels of OsAKT1 mRNA, encoding a K transporter. We also found a negative relationship between shoot Cs and K status in control-N but not in low-N conditions. Our results suggest that the application of N shifts Cs from roots into the shoots and that OsAKT1 in root vascular tissues influences Cs allocation. In practice, fine tuning N/K application and targeted breeding of K transporters might mitigate Cs contamination in rice plants.

The thermal denaturation of ribonuclease A in aqueous-methanol solvents.

Circular dichroism was used to monitor the thermal unfolding of ribonuclease A in 50% aqueous methanol. The spectrum of the protein at temperatures below -10 degrees C (pH* 3.0) was essentially identical to that of native ribonuclease A in aqueous solution. The spectrum of the thermally denatured material above 70 degrees C revealed some residual secondary structure in comparison to protein unfolded by 5 M Gdn.HCl at 70 degrees C in the presence or absence of methanol. The spectra as a function of temperature were deconvoluted to determine the contributions of different types of secondary structure. The position of the thermal unfolding transition as monitored by alpha-helix, with a midpoint at 38 degrees C, was at a much higher temperature than that monitored by beta-sheet, 26 degrees C, which also corresponded to that observed by delta A286, tyrosine fluorescence and hydrodynamic radius (from light scattering measurements). Thus, the loss of beta-sheet structure is decoupled from that of alpha-helix, suggesting a step-wise unfolding of the protein. The transition observed for loss of alpha-helix coincides with the previously measured transition for His-12 by NMR from a partially folded state to the unfolded state, suggesting that the unfolding of the N-terminal helix in RNase A is lost after unfolding of the core beta-sheet during thermal denaturation. The thermally denatured protein was relatively compact, as measured by dynamic light scattering.

Secondary structure formation precedes tertiary structure in the refolding of ribonuclease A.

The kinetics of refolding of ribonuclease A were monitored by circular dichroism (CD), tyrosine fluorescence and absorbance in the -40 to -10 degrees C range using a methanol cryosolvent. The native-like far-ultraviolet CD signal returned in the dead-time of the mixing, whereas the native absorbance and fluorescence signals returned in a multiphasic process at rates several orders of magnitude more slowly. Thus the secondary structure was formed much more rapidly than the tertiary structure. In addition, the absorbance signal showed evidence of an early intermediate in which one, or more, tyrosine residues was in a transiently more polar environment. A total of four kinetic phases were observed by absorbance in refolding, the slowest two of which had energies of activation consistent with proline isomerization. A refolding scheme involving initial hydrophobic collapse, concurrent with secondary structure formation, followed by much slower rearrangement to the native tertiary structure is proposed.

Protein sequence entropy is closely related to packing density and hydrophobicity.

We investigated the correlation between the Shannon information entropy, 'sequence entropy', with respect to the local flexibility of native globular proteins as described by inverse packing density. These are determined at each residue position for a total set of 130 query proteins, where sequence entropies are calculated from each set of aligned residues. For the accompanying aggregate set of 130 alignments, a strong linear correlation is observed between the calculated sequence entropy and the corresponding inverse packing density determined at an associated residue position. This region of linearity spans the range of C(alpha) packing densities from 12 to 25 amino acids within a sphere of 9 angstrom radius. Three different hydrophobicity scales all mimic the behavior of the sequence entropies. This confirms the idea that the ability to accommodate mutations is strongly dependent on the available space and on the propensity for each amino acid type to be buried. Future applications of these types of methods may prove useful in identifying both core and flexible residues within a protein.

The effect of methanol and temperature on the kinetics of refolding of ribonuclease A.

Unfolded ribonuclease A consists of 20% fast refolding (Uf) and 80% slow refolding material (Us). The latter consists of at least two different forms which refold at different rates. We have used absorbance and fluorescence spectrophotometry to compare the kinetics of refolding in aqueous and aqueous-methanol solutions. At 1 degree C and pH 3.0, the addition of increasing concentrations of methanol (to 50%, v/v) had negligible effect on the rates and amplitudes of the slow refolding Us states. The effect of temperature on the two slow phases of refolding was determined in 35 and 50% methanol. From Arrhenius plots the energies of activation were found to be in the vicinity of 20 kcal/mol for both processes. The results suggest that both slow phases correspond to proline isomerization, and that the presence of methanol does not significantly perturb the overall refolding process. It is possible that the faster of the slow refolding phases corresponds to the isomerization of a proline residue which is trans in the folded native state but which undergoes extensive isomerization to the cis conformation in the unfolded state.

Biological applications of hammerhead ribozymes as anti-viral molecules.

Ribozymes are catalytic RNAs that can cleave substrate RNAs in a sequence specific manner. Here we survey, in brief, the structure of hammerhead and hairpin ribozymes and discuss their applications as molecular antiviral molecules for HIV-1.

The Wnt signaling pathway and its role in tumor development.

Cancer development depends on the aberrant activation of signal transduction pathways that control cell growth and survival and play important roles in normal embryonic development. This review will focus on one of the most powerful pathways, the canonical Wnt signal transduction cascade, which has been originally described in vertebrate and non-vertebrate embryogenesis and subsequently associated with the development of a multitude of different tumor types, mainly of gastrointestinal origin. In recent years, a variety of novel interacting components and functions have been identified in the Wnt pathway revealing not only the complexity of Wnt signaling but also its potency. Here we will concentrate on the role of the Wnt pathway in cancer development with emphasis placed on the molecular defects known to promote neoplastic transformation in humans and in animal models.

Conformations of t-RNA: base pairing and stacking.

The Phe t-RNA structure can be fit with one point per nucleotide to lattice models, and a fit for the 76 points to a face-centered cubic lattice is achieved with an RMS of 1.76 A. There are 32 chain folds possible upon these points. Because it is impossible to calculate directly all combinations of potential base pairs for these cases, an alternative is to determine low energy secondary structures and subsequently the tertiary pairs. For each lattice fold, the low energy secondary structures are generated from a list of proximal bases. From the lists of remaining possible tertiary pairs, all combinations are generated, and these include 2,365,440 allowed conformers. Among the possible types of non-native conformational variations observed is slip pairing, accompanied by a bulge, at the end of a stem. Small changes in secondary structure can result in different tertiary pairs. Other calculations, not constrained to the t-RNA shape, are presented that involve the packing of rigid stems on a flexible internal loop. For a simple cubic lattice there are 36,484,128 lattice folds for the sixteen bases enclosing the internal loop. By attaching rigid stems and accounting for their excluded volume these are reduced to only 258,979 possible configurations. The most common stacking arrangements involve the usual two pairs of stacked stems indicated in the crystal structure. The present enumerations suggest that a completely thorough exploration of three dimensional RNA structures is feasible only with prior specification of restrictions on conformational freedom, such as those given by secondary structures.

Suffering, sovereignty, and the purposes of God: Christian convictions and medical killing.

Despite a variety of "non-ecumenical" features in Christian arguments about suicide, assisted suicide, and euthanasia, there are obvious "ecumenical" aspects to be found in the general Christian prohibition of these practices. A fair reading of the Christian tradition requires that we acknowledge both the differences that distinguish particular perspectives and the fundamental themes that allow an identifiably Christian position to emerge in stark contrast to the secular discussion of these issues. Central to Christian interpretations of dying and death are an acknowledgment of God's sovereignty over human life, an understanding of suffering that stresses identification with Christ as the source of Christian hope, and the recognition that God's creative and redemptive purposes are generally (or always) at odds with the deliberate choice of assisted suicide or euthanasia.

Sexual ethics and communal judgments: on the pluralism of virtues, values, and practices.

Different judgments by Christian communities on issues in sexual ethics involve different weightings of various sources of moral authority, different understandings of the normativity of the natural, and different assessments of the scope of freedom to be exercised in relation to the goods of marriage. These fundamental differences of interpretation can be exemplified by the ongoing Roman Catholic discussion of the legitimacy of voluntary sterilization in certain "hard cases." The contributors to this issue of Christian Bioethics, in their spirited exchange on that issue, exemplify the need for careful attention to the ways that differences of theological emphasis and moral method lead to different judgements in particular cases, both within and between particular Christian communities.

The common good in a secular society: the relevance of a Roman Catholic notion to the healthcare allocation debate.

This essay analyzes Roman Catholic social teaching on the right to health care and the legitimacy of healthcare rationing. It considers that discussion at two levels: (1) the specific warrants that undergrid key terms; and (2) the accessibility and applicability of those warrants to policy choices in a secular society. The essay concludes with a number of broader reflections meant to reserve an appropriate place for religious voices in the process of policy-making, as distinguished from its justification.

Perseverations on a critical theme.

In response to my earlier critique of recent attempts to rebut principlism as an ethical approach, Green, Gert, and Clouser (GG&C) have in turn offered their own critique of my appraisal. This essay identifies eight major criticisms GG&C raise in their response and offers a rejoinder to each. Among them, three are especially important: (1) that the label of 'deductivism' fails to capture GG&C's ethical method and should be replaced by 'descriptivism'; (2) that pluralistic accounts, including principlism, fail to offer any systematic way to resolve moral conflicts; and (3) that appeals to broader 'moral' principles beyond the moral rules are deceiving, since apparent differences in 'moral' judgment invariably involve disagreement about empirical facts rather than further moral considerations. In response to (1), I defend my earlier label by emphasizing the stipulated and invariant status of the moral rules GG&C invoke, even as I question the adequacy of their putative 'descriptivism'. In response to (2), I suggest the plausibility of pluralist approaches and reiterate the modified just-war criteria that Beauchamp and Childress invoke in situations when principles conflict. In response to (3), I suggest that a 'descriptivism' worthy of the name must systematically accommodate the appeal to moral principles that remains central to metaethical and normative discussions.

The method of 'principlism': a critique of the critique.

Several scholars have recently criticized the dominant emphasis upon mid-level principles in bioethics best exemplified by Beauchamp and Childress's Principles of Biomedical Ethics. In Part I of this essay, I assess the fairness and cogency of three broad criticisms raised against 'principlism' as an approach: (1) that principlism, as an exercise in applied ethics, is insufficiently attentive to the dialectical relations between ethical theory and mortal practice; (2) that principlism fails to offer a systematic account of the principles of non-maleficence, beneficence, respect for autonomy, and justice; and (3) that principlism, as a version of moral pluralism, is fatally flawed by its theoretical agnosticism. While acknowledging that Beauchamp and Childress's reliance upon Ross's version of intuitionism is problematic, I conclude that the critics of principlism have failed to make a compelling case against its theoretical or practical adequacy as an ethical approach. In Part II, I assess the moral theory developed by Bernard Gert in Mortality: A New Justification of the Moral Rules, because Gert has recommended his approach as a systematic alternative to principlism. I judge Gert's theory to be seriously incomplete and, in contrast to principlism, unable to generate coherent conclusions about cases of active euthanasia and paternalism.

Consistencies of individual DNA base-amino acid interactions in structures and sequences.

Amino acid-amino acid interaction energies have been derived from crystal structure data for a number of years. Here is reported the first derivation of normalized relative interaction from binding data for each of the four bases interacting with a specific amino acid, utilizing data from combinatorial multiplex DNA binding of zinc finger domains [Desjarlais, J. R. and Berg, J. M. (1994) Proc. Natl. Acad. Sci. USA, 91, 11099-11103]. The five strongest interactions are observed for lysine-guanine, lysine-thymine, arginine-guanine, aspartic acid-cytosine and asparagine-adenine. These rankings for interactions with the four bases appear to be related to base-amino acid partial charges. Also, similar normalized relative interaction energies are derived by using DNA binding data for Cro and lambda repressors and the R2R3 c-Myb protein domain [Takeda, Y., Sarai, A. and Rivera, V. M. (1989) Proc. Natl. Acad. Sci. USA, 86, 439-443; Sarai, A. and Takeda, Y. (1989) Proc. Natl. Acad. Sci. USA, 86, 6513-6517; Ogata, K. et al. (1995) submitted]. These energies correlate well with the combinatorial multiplex energies, and the strongest cases are similar between the two sets. They also correlate well with similar relative interaction energies derived directly from frequencies of bases in the bacteriophage lambda operator sequences. These results suggest that such potentials are general and that extensive combinatorial binding studies can be used to derive potential energies for DNA-protein interactions.

RNA base-amino acid interaction strengths derived from structures and sequences.

We investigate RNA base-amino acid interactions by counting their contacts in structures and their implicit contacts in various functional sequences where the structures can be assumed to be preserved. These frequencies are cast into equations to extract relative interaction energetics. Previously we used this approach in considering the major groove interactions of DNA, and here we apply it to the more diverse interactions observed in RNA. Structures considered are the three different tRNA synthetase complexes, the U1A spliceosomal protein with an RNA hairpin and the BIV TAR-Tat complex. We use binding data for the base frequencies for the seryl, aspartyl and glutaminyl tRNA-synthetase and U1 RNA-protein complexes. We compare with the previously reported DNA major groove peptide contacts the results for atoms of RNA bases, usually in the major groove. There are strong similarities between the rank orders of interacting bases in the DNA and the RNA cases. The apparent strongest RNA interaction observed is between arginine and guanine which was also one of the strongest DNA interactions. The similar data for base atomic interactions, whether base paired or not, support the importance of strong atomic interactions over local structure considerations, such as groove width and alpha-helicity.

RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access.

For the binding of peptides to wild-type HIV-1 and BIV TAR RNA and to mutants with bulges of various sizes, changes in the DeltaDelta G values of binding were determined from experimental K d values. The corresponding entropies of these bulges are estimated by enumerating all possible RNA bulge conformations on a lattice and then applying the Boltzmann relationship. Independent calculations of entropies from fluctuations are also carried out using the Gaussian network model (GNM) recently introduced for analyzing folded structures. Strong correlations are seen between the changes in free energy determined for binding and the two different unbound entropy calculations. The fact that the calculated entropy increase with larger bulge size is correlated with the enhanced experimental binding free energy is unusual. This system exhibits a dependence on the entropy of the unbound form that is opposite to usual binding models. Instead of a large initial entropy being unfavorable since it would be reduced upon binding, here the larger entropies actually favor binding. Several interpretations are possible: (i) the higher conformational freedom implies a higher competence for binding with a minimal strain, by suitable selection amongst the set of already accessible conformations; (ii) larger bulge entropies enhance the probability of the specific favorable conformation of the bound state; (iii) the increased freedom of the larger bulges contri-butes more to the bound state than to the unbound state; (iv) indirectly the large entropy of the bound state might have an unfavorable effect on the solvent structure. Nonetheless, this unusual effect is interesting.