Constructive Neutral Evolution is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic and molecular structures (...) or processes, such as retained gene duplications, the spliceosome, and RNA editing. Here we aim to expand the scope of such explanation beyond the molecular level, integrating CNE with Multi-Level Selection theory, and arguing that several popular higher-level selection scenarios are in fact instances of CNE. Suitably contextualized, CNE occurs at any level in the biological hierarchy at which natural selection as normally construed occurs. As examples, we focus on modularity in protein–protein interaction networks or “interactomes,” the origin of eukaryotic cells and the evolution of co-dependence in microbial communities—a variant of the “Black Queen Hypothesis” which we call the “Gray Queen Hypothesis”. (shrink)

Recent debates about the biological and evolutionary conditions for sentience have generated a renewed interest in fine-grained functionalism. According to one such account advanced by Peter Godfrey-Smith, sentience depends on the fine-grained activities characteristic of living organisms. Specifically, the scale, context and stochasticity of these fine-grained activities. One implication of this view is that contemporary artificial intelligence is a poor candidate for sentience. Insofar as current AI lacks the ability to engage in such living activities it will lack sentience, no (...) matter what its coarse-grained functions. In this paper, we review the case for fine-grained functionalism and show that there are contemporary machines that fulfil the fine-grained functional criteria identified by Godfrey-Smith, and thus are candidates for sentience. Molecular machines such as Brownian computers are analogous to metabolic activity in their scale, context and stochasticity, and can serve as the basis of AI. Molecular computation is a promising candidate for artificial sentience according to contemporary philosophical accounts of sentience. (shrink)

Constructive Neutral Evolution theory provides selectively neutral explanations of the origin and maintenance of biological complexity. This essay provides an analysis of CNE as an explanatory strategy defined by a tripartite set of conditions, and shows how this applies to cases of the evolution of complexity at higher-levels of the biological hierarchy. CNE was initially deployed to help explain a variety of complex molecular structures and processes, including spliceosomal splicing, trypansomal pan-editing, scrambled genes in ciliates, duplicate gene retention and fungal (...) ATP synthetase structure. CNE has also been generalized to apply to phenomena at the cellular level, including protein-protein interaction network modularity, obligate microbial symbioses, eukaryogenesis and microbial unculturability. This essay further extends CNE to cases of complexity at levels of organization higher than the molecular and cellular. These are multicellular phenotypic complexity, multicellular ecological complexity and, some cases of cultural complexity. (shrink)

We begin with the idea that lines of reasoning are continuous mental processes and develop a notion of continuity in proof. This requires abstracting the notion of a proof as a set of sentences ordered by provability. We can then distinguish between discrete steps of a proof and possibly continuous stages, defining indexing functions to pick these out. Proof stages can be associated with the application of continuously variable rules, connecting continuity in lines of reasoning with continuously variable reasons. Some (...) examples of continuous proofs are provided. We conclude by presenting some fundamental facts about continuous proofs, analogous to continuous structural rules and composition. We take this to be a development on its own, as well as lending support to non-finitistic constructionism. (shrink)

In the 1970s, R.D. MacElroy coined the term ‘extremophile’ to describe microorganisms that thrive under extreme conditions (MacElroy 1974). This hybrid word transliterates to ‘love of extremes’ and has been studied as a straightforward concept for the past 40 years. In this paper, we discuss several ways the term has been understood in the scientific literature, each of which has different consequences for the distribution and importance of extremophiles. They are, briefly, Human-Centric, at the Edge of life’s habitation of Morphospace, (...) by appeal to Statistical Rarity, described by Objective Limits, and at the Limits of Impossibility for metabolic processes. Importantly, these concepts have co-existed, unacknowledged and conflated, for decades. Confusion and equivocation threaten to follow from the wildly varied inclusion or exclusion of organisms as extremophiles depending on the concept used. Under some conceptions, entire kinds of extremophiles become meaningless. Since our understanding of how life works is shaped by what we take to be its extremes, clarifying extremophily is key for many large-scale projects in biology, ecology, biotechnology and astrobiology. In what follows, we proceed as if a noncontroversial account of life is possible and that it is possible to find complex chemistry in the Universe that is similar enough to Life on Earth such that both may be considered instances of ‘life’ (but see Mariscal & Doolittle 2018). We raise, but do not address, the questions of whether the distribution of Life on Earth is representative of what we may find elsewhere in the Universe, whether the same kinds of extremophiles would exist given a replay of the tape of life. Additionally, each of these concepts assumes life based on some sort of biochemistry in this universe, effectively setting aside claims made by some artificial life proponents that their digital organisms are genuine examples of life (Langton 1989, Ray 1995). On the distinction between extremophilic and extremotolerant, we note that all accounts accept the latter as a broader category than the former, since ‘phily’ means love and tolerance is a prerequisite for love under any conception. Indeed, there will be many extremely impoverished environments where tolerance is the only option and thriving is precluded, e.g. Bacillus marismortui was extracted and grown from 250-million-year-old salt crystals in the Permian Salado Formation in an inactive yet persistent state (Vreeland et al., 2000). We also note that extremophily, as a functional category, is potentially applicable at many levels of the biological hierarchy. Extremophily at one level does not necessarily extend to higher and lower levels. For instance, a microorganism in isolation might be quite intolerant to certain environmental conditions yet flourish when subjected to the same conditions as a community or natural biofilm. Alternatively, a protein molecule might be quite stable or active under certain conditions even if the optimal environment for the organism containing it is far more mesophilic. There is an industry of artificially selecting organisms and proteins to adapt to extreme environments (see van den Burg & Eijsink 2002), providing some justification to consider ‘functioning at extremes’ as a worthwhile category of investigation. Finally, we also note certain physico-chemical ranges are rarely considered with respect to extremophily – timespan, size, nutrient availability (Hoehler & Jørgensen 2013), etc. – as well as some biological parameters – abundance, isolation, competition, etc. Perhaps scientific interest must also come into play as to the reason these criteria are not considered relevant. We return to this issue later. In the next section, we give five definitions of extremophily, show their benefits, drawbacks, and unintended yet unavoidable consequences. These arguments are summarized in Table 1 and represented visually in Figures 1 and 2. Given research on polyextremophiles, it seems Figure 2 is a more plausible representation of the state of current knowledge than Figure 1 (Harrison et al. 2013). Life is patchily distributed across various dimensions, which may reflect its contingent history, poor sampling, or (perhaps) fundamental limits. Figure 3 shows the conceptual flowchart for all of these views. In the following section, we take a step back to ask whether we should choose between these definitions and how such a judgment could be made. We argue for a limited pluralism, in which some, but not all, of the concepts are acceptable relative to certain practical and theoretical aims. (shrink)

Microbiologists are transitioning from the study and characterization of individual strains or species to the profiling of whole microbiomes and microbial ecology. Equipped with high-throughput methods for studying the taxonomic and functional characteristics of diverse samples, they are just beginning to encounter the conceptual, theoretical, and experimental problems of comparing taxonomy to function, and extracting useful measures from such comparisons. Although still unresolved, these problems are well studied in macro-ecology and are reiterated here as an historical precautionary for microbial ecologists. (...) Beyond expected and unresolved terminological vagueness, we argue that assessments and comparisons of taxonomic and functional profiles in micro-ecology suffer from theoretically unresolvable arbitrariness and ambiguities. We divide these into problems of scale, individuation, and commensurability. We argue that there is no technically/theoretically “correct” scale, individuation, or comparison of taxonomy and function, but there are nonetheless better and worse methodologies for profiling. (shrink)

We argue that artificial networks are explainable and offer a novel theory of interpretability. Two sets of conceptual questions are prominent in theoretical engagements with artificial neural networks, especially in the context of medical artificial intelligence: Are networks explainable, and if so, what does it mean to explain the output of a network? And what does it mean for a network to be interpretable? We argue that accounts of “explanation” tailored specifically to neural networks have ineffectively reinvented the wheel. In (...) response to, we show how four familiar accounts of explanation apply to neural networks as they would to any scientific phenomenon. We diagnose the confusion about explaining neural networks within the machine learning literature as an equivocation on “explainability,” “understandability” and “interpretability.” To remedy this, we distinguish between these notions, and answer by offering a theory and typology of interpretation in machine learning. Interpretation is something one does to an explanation with the aim of producing another, more understandable, explanation. As with explanation, there are various concepts and methods involved in interpretation: Total or Partial, Global or Local, and Approximative or Isomorphic. Our account of “interpretability” is consistent with uses in the machine learning literature, in keeping with the philosophy of explanation and understanding, and pays special attention to medical artificial intelligence systems. (shrink)

In 1885, during initial discussions of J. C. Maxwell's celebrated thermodynamic demon, Whiting (1) observed that the demon-like velocity selection of molecules can occur in a gravitationally bound gas. Recently, a gravitational Maxwell demon has been proposed which makes use of this observation [D. P. Sheehan, J. Glick, and J. D. Means, Found. Phys. 30, 1227 (2000)]. Here we report on numerical simulations that detail its microscopic phase space structure. Results verify the previously hypothesized mechanism of its paradoxical behavior. This (...) system appears to be the only example of a fully classical mechanical Maxwell demon that has not been resolved in favor of the second law of thermodynamics. (shrink)

In a recent reply to our article, “What is Interpretability?,” Prasetya argues against our position that artificial neural networks are explainable. It is claimed that our indefeasibility thesis—that adding complexity to an explanation of a phenomenon does not make the phenomenon any less explainable—is false. More precisely, Prasetya argues that unificationist explanations are defeasible to increasing complexity, and thus, we may not be able to provide such explanations of highly complex AI models. The reply highlights an important lacuna in our (...) original paper, the omission of the unificationist account of explanation, and affords us the opportunity to respond. Here, we argue that artificial neural networks are explainable in a way that should satisfy unificationists and that interpretability methods present ways in which ML theories can achieve unification. (shrink)

In 2000, a simple, foundational thermodynamic paradox was proposed: a sealed blackbody cavity contains a diatomic gas and a radiometer whose apposing vane surfaces dissociate and recombine the gas to different degrees (A $_{2} \rightleftharpoons $ 2A). As a result of differing desorption rates for A and A $_{2}$ , there arise between the vane faces permanent pressure and temperature differences, either of which can be harnessed to perform work, in apparent conflict with the second law of thermodynamics. Here we (...) report on the first experimental realization of this paradox, involving the dissociation of low-pressure hydrogen gas on high-temperature refractory metals (tungsten and rhenium) under blackbody cavity conditions. The results, corroborated by other laboratory studies and supported by theory, confirm the paradoxical temperature difference and point to physics beyond the traditional understanding of the second law. (shrink)

Based on concepts of self-organization, we interpret apparent motion as the result of a so-called non-equilibrium phase transition of the perceptual system with the stimulus-onset asynchrony (SOA) acting as a control parameter. Accordingly, we predict a significantly increasing variance of the quality index of apparent motion close to critical SOAs. [Shepard].

The counterfactual and regularity theories are universal accounts of causation. I argue that these should be generalized to produce local accounts of causation. A hallmark of universal accounts of causation is the assumption that apparent variation in causation between locations must be explained by differences in background causal conditions, by features of the causal-nexus or causing-complex. The local account of causation presented here rejects this assumption, allowing for genuine variation in causation to be explained by differences in location. I argue (...) that local accounts of causation are plausible, and have pragmatic, empirical and theoretical advantages over universal accounts. I then report on the use of presheaves as models of local causation. The use of presheaves as models of local variation has precedents in algebraic geometry, category theory and physics; they are here used as models of local causal variation. The paper presents this idea as stemming from an approach using presheaves as models of local truth. Finally, I argue that a proper balance between universal and local causation can be assuaged by moving from presheaves to fully-fledged sheaf models. (shrink)

The current conception of the plurality of worlds is founded on a set theoretic understanding of possibilia. This paper provides an alternative category theoretic conception and argues that it is at least as serviceable for our understanding of possibilia. In addition to or instead of the notion of possibilia conceived as possible objects or possible individuals, this alternative to set theoretic modal realism requires the notion of possible morphisms, conceived as possible changes, processes or transformations. To support this alternative conception (...) of the plurality of worlds, I provide two examples where a category theoretic account can do work traditionally done by the set theoretic account: one on modal logic and another on paradoxes of size. I argue that the categorial account works at least as well as the set theoretic account, and moreover suggest that it has something to add in each case: it makes apparent avenues of inquiry that were obscured, if not invisible, on the set theoretic account. I conclude with a plea for epistemological humility about our acceptance of either a category-like or set-like realist ontology of modality. (shrink)

Traditional epistemic and doxastic logics cannot deal with inconsistent beliefs nor do they represent the evidence an agent possesses. So-called ‘evidence logics’ have been introduced to deal with both of those issues. The semantics of these logics are based on neighbourhood or hypergraph frames. The neighbourhoods of a world represent the basic evidence available to an agent. On one view, beliefs supported by evidence are propositions derived from all maximally consistent collections evidence. An alternative concept of beliefs takes them to (...) be propositions derivable from consistent partitions of one’s inconsistent evidence; this is known as Schotch-Jennings Forcing. This paper develops a modal logic based on the hypergraph semantics to represent Schotch-Jennings Forcing. The modal language includes an operator U(φ1,…,φn;ψ)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$U(\varphi _1, \ldots, \varphi _n;\psi )$$\end{document} which is similar to one introduced in Instantial Neighbourhood Logic. It is of variable arity and the input formulas enjoy distinct roles. The U operator expresses that all evidence at a particular world that supports ψ\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\psi $$\end{document} can be supported by at least one of the φi\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\varphi _i$$\end{document}s. U can then be used to express that all the evidence available can be unified by the finite set of formulas φ1,…,φn\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\varphi _1,\ldots, \varphi _n$$\end{document} if ψ\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\psi $$\end{document} is taken to be ⊤\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\top $$\end{document}. Future developments will then use that semantics as the basis for a doxastic logic akin to evidence logics. (shrink)

This introduction to the philosophy of science includes six chapters, each taking up a single problem—though the last four constitute something of a package: three attempts to establish Schlesinger’s criterion of confirmability, four applies it to non-confirmable sentences in such a way as to provide an alternative to the Wittgensteinian "received view" about the meaningless of self-referring sentences; in the process Schlesinger defends a version of neo-verificationism which, in five and six, he attempts to show is nontrivial by applying it (...) to the discussion of the nature of time and of determinism. To complete the list, chapter two discusses confirmation and parsimony ; and chapter one is introductory, discussing Niced’s criterion and Hempel’s paradox in terms of "the most simple type of generalization... ‘All ravens are black'... found mainly in elementary science or commonsense, prescientific reasoning". (shrink)

What MacKinnon offers here is a provocative and original analysis of the meaning of the word "true." His applications are in the areas of statements in general, scientific theories, and theological propositions. One reason for the interest of the book can be found in MacKinnon’s intellectual odyssey. Setting out from a starting-point of standard neo-scholastic textbook philosophy and theology, MacKinnon has come to a highly personal synthesis to which he is willing at least tentatively to apply the label, "ontological pragmatism." (...) Stages along the way—and elements in the synthesis—include Bernard Lonergan’s transcendental Thomism, Wilfrid Sellars’ neo-Kantian version of analytical epistemology, and much detailed work of MacKinnon’s own in analytical philosophy of science. The provocative character of Truth and Expression is likely to bring criticism of the author for misuse of his sources. Wittgensteinian philosophical therapists are likely to bemoan MacKinnon’s relapse into ontologism, even if he qualifies it as a "pragmatic" version. Sellars is likely to object to being lumped with Lonergan, and the latter would probably be upset with the uses to which his former student has put his insights. It may also be worthwhile here to express a demur or two with respect to MacKinnon’s use of his Thomistic sources, e.g., concerning his theory of meaning. It seems that MacKinnon has accepted too naively what might best be called "textbook Thomism." It is true that Aquinas offers a mentalist view, and true also that both Aristotle and Aquinas speak of words as signs of concepts. While this can give rise to a private-language mentalism of the kind Wittgenstein would criticize, it must be recalled that Aristotle and Aquinas were writing not only before Wittgenstein but also before Kant. Whatever can be said of Aquinas’ "mentalism," it is certainly true that in other contexts Aquinas has a social theory of learning that is, at least on the surface, incompatible with a private language theory. Again, with respect to theological truth it seems likely that MacKinnon has been misled by Thomistic manuals, at least when he claims that what Aquinas offers is "a geometrically ordered deductive system" in which "the primacy of Jesus as a revelation of God does not fit." Historical studies of the function of his Summa Theologiae in Aquinas’ scheme for theological education do not support the view of Aquinas as a theological deductive system builder. Nor is it true, as MacKinnon seems to hold, that Aquinas’ view of theological truth is more Aristotelian than biblical. Aside from these qualifications on his use of sources, MacKinnon’s book offers an abundance of critical thinking, analytical insight, and systematic ability. For instance, the reader interested in MacKinnon’s original approach to an adequate epistemology of science will here, in chapter three of Truth and Expression, find the best summary yet of his many contributions in that area. Whether or not, in the last analysis, MacKinnon’s synthesis will be historically significant remains to be seen. What seems likely now is that if it does, the ingredient elements of Lonergen, [[sic]] Sellars, Wittgenstein, Quine, etc., will be more muted, and MacKinnon’s own synthesis will stand on its own. Meanwhile, Truth and Expression will serve as the best guide, pointing in the direction we can expect MacKinnon to follow in the future.—P. T. D. (shrink)

Since Doob rules out philosophical puzzles as to the nature of time, its absolute or relative character, or its universality and direction, etc., this masterful work will be of only limited interest to philosophers, even those who specialize in problems of space and time. Patterning of Time is, however, a fascinating study from the perspective of a psychologist or anthropologist. Doob, whose overwhelming knowledge has been gained as much from the library as from laboratory and field research, ranges over a (...) vast area, both in terms of literature surveyed and in terms of the variety of aspects of time perception studied. He spells out his principal thesis this way: "My principal thesis now emerges, it is hoped: we experience in the psychological present, even as we recollect the past and anticipate the future; and at any given moment, and sometimes over long periods, we renounce one of these activities as a result of one or both of the other two orientations. Temporal judgments which perforce occur in the psychological present are patterned by beliefs and attitudes which are recollected from the past and which affect future anticipations. We are always—or almost always—confronted with choices in time, and to choose we must renounce.". (shrink)

There is evidence that asexual reproduction has a long-term disadvantage when compared to sexual reproduction. This disadvantage is usually assumed to arise from the more efficient incorporation of advantageous mutations by sexual populations. We consider here the effect on asexual and sexual populations of changes in the fitness of harmful mutations. It is shown that the re-establishment of equilibrium following environmental change is generally faster in sexual populations, and that the mutational load experienced by the sexual population can be significantly (...) less during this period than that experienced by an asexual one. Changes in the fitness of harmful mutations may therefore impose a greater long-term disadvantage on asexual populations than those which are sexual. (shrink)

A critical discussion is provided of three central assumptions underlying Nunez's approach to modeling cortical activity. A plea is made for neurophysiologically realistic models involving nonlinearities, multiple time scales, and stochasticity.

In 1885, during initial discussions of J. C. Maxwell's celebrated thermodynamic demon, Whiting(1) observed that the demon-like velocity selection of molecules can occur in a gravitationally bound gas. Recently, a gravitational Maxwell demon has been proposed which makes use of this observation [D. P. Sheehan, J. Glick, and J. D. Means, Found. Phys. 30, 1227 (2000)]. Here we report on numerical simulations that detail its microscopic phase space structure. Results verify the previously hypothesized mechanism of its paradoxical behavior. This system (...) appears to be the only example of a fully classical mechanical Maxwell demon that has not been resolved in favor of the second law of thermodynamics. (shrink)

Aim: Patients with advanced cancer need information about end-of-life treatment options in order to make informed decisions. Clinicians vary in the frequency with which they initiate these discussions.Patients and methods: As part of a long-term longitudinal study, patients with an expected 2-year survival of less than 50% who had advanced gastrointestinal or lung cancer or amyotrophic lateral sclerosis were interviewed. Each patient’s medical record was reviewed at enrollment and at 3 months for evidence of the discussion of patient wishes concerning (...) ventilator support, artificial nutrition and hydration , resuscitation and hospice care. A Kaplan–Meier analysis was also performed and 2-year survival calculated.Results: 60 cancer and 32 ALS patients were enrolled. ALS patients were more likely than cancer patients to have evidence of discussion about their wishes for ventilator support , ANH , DNR and hospice care . At 6 months, 91% of ALS patients were alive compared with 62% of cancer patients; at 2 years, 63% of ALS patients were alive compared with 23% of cancer patients .Conclusions: Cancer patients were less likely than ALS patients to have had documented advanced care planning discussions despite worse survival. This may reflect perceptions that ALS has a more predictable course, that advanced cancer has a greater number of treatment options, or differing views about hope. Nevertheless, cancer patients may be less adequately prepared for end-of-life decision-making. (shrink)

Philosophical Studies Vol. 2, No. 2, p. 163, l. 24 for ‘Pocreon’ read “Creon’ and p. 165, l.4 for “Nereus” read “Nessus”, l. 16 for “Corrolate” read “Correlate” and l. 27 for “ Trachinae ” read “ Trachiniae ”. Proffessor Mackinnon should also have been described as Norris-Hulse Professor of Divinity in the University of Cambridge and Fellow of Corpus Christi College.

The volume presents essays on the philosophical explanation of the relationship between body and soul in antiquity from the Presocratics to Galen. The title of the volume alludes to a phrase found in Plato, Aristotle and Plotinus, referring to aspects of living behaviour involving both body and soul, and is a commonplace in ancient philosophy, dealt with in very different ways by different authors.

A total of 944 expressed sequence tags generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat. EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and ID with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms (...) was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences, where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses. (shrink)

Objectives The objectives of the study are to understand the current practice of informed consent in medical research in public hospitals in Shanghai, and to share our views with other countries, especially developing countries. Methods In the study, 145 consent forms (CFs) of the selected research projects in eight public hospitals with ethics committees in Shanghai were audited, and the principle investigators (PIs) of these research projects and 40 student subjects who had participated in clinical drug tests were surveyed by (...) questionnaires. Results The CFs of medical researches in public hospitals with ethics committees in Shanghai were generally acceptable. However, there were some defects in the CFs. Although most of the surveyed PIs had correct recognition of informed consent, some processes of informed consent were not in accordance with generally accepted requirements. A large number of the PIs considered the greatest difficulty with informal consent was lack of correct recognition of subjects or legally authorised representatives on medical research. Discussion Informed consent in medical research should consider the research ethics, the background of potential subjects, the local resources and culture of medical research. In addition, special protection is needed for student subjects in informed consent as well as efforts for building and restoring the public's trust in biomedical research. Conclusion The informed consent in Shanghai's public hospitals with ethics committees was generally acceptable and the achievement of adequate informed consent is influenced by many factors. (shrink)