Speciation by physiological selection of environmentally acquired traits

A chance mutation affecting a single or extremely few individuals in a continuous population will be quickly diluted through interbreeding. Charles Darwin fully appreciated this difficulty with relying on natural selection alone, and suggested an enabling role for geographical isolation in the origin of species. However, Darwin also believed in evolution by the inheritance of acquired traits and in populations of interbreeding animals, both of which would need a different isolating mechanism to overcome dilution and play a role in animal evolution. Historically disputed, the inheritance of acquired characters is now increasingly accepted as a phenomenon, and Charles Darwin himself is acknowledged as closely pre-empting the type of physiology necessary to mediate it in his hypothesis of 'pangenesis'. In this article, we question how the inheritance of acquired traits might overcome the problem of dilution by interbreeding and contribute to evolution. Specifically, we describe how Darwin's young protégé, George Romanes, developed ideas he discussed with Darwin and extended pangenesis to include a conceivable solution published after Darwin's death: physiological selection of fertility. In light of the 'rediscovery' of pangenesis, here we recount physiological selection as a testable hypothesis to explain how environmentally acquired characteristics could become coupled to the generation of species.

Bubbling beyond the barrier: exosomal RNA as a vehicle for soma-germline communication

'Weismann's barrier' has restricted theories of heredity to the transmission of genomic variation for the better part of a century. However, the discovery and elucidation of epigenetic mechanisms of gene regulation such as DNA methylation and histone modifications has renewed interest in studies on the inheritance of acquired traits and given them mechanistic plausibility. Although it is now clear that these mechanisms allow many environmentally acquired traits to be transmitted to the offspring, how phenotypic information is communicated from the body to its gametes has remained a mystery. Here, we discuss recent evidence that such communication is mediated by somatic RNAs that travel inside extracellular vesicles to the gametes where they reprogram the offspring epigenome and phenotype. How gametes learn about bodily changes has implications not only for the clinic, but also for evolutionary theory by bringing together intra- and intergenerational mechanisms of phenotypic plasticity and adaptation.

Impoverished Conceptions of Gene Causation and Therapy in Developmental Neurology

We offer a primer to the modifiability of genetic neurological disease, particularly during development. One goal is to harness several unexpected observations made in the course of experimental gene modification or therapy into an explanatory conceptual context based on biological first principles. To this end, we anchor growing, disparate reports of unusual or untoward effects to a plausible framework wherein genes exhibit different degrees of modifiability and may result, when mutated or therapeutically modified, in unsuspected consequences. We propose that genetic pathogenic variant effects and modifiability depend on the number and complexity of associated protein-protein or higher-order interactions. Thus, gene malleability may range from that characteristic of the favorably modifiable primarily structural genes that subserve relatively invariant or circumscribed phenomena such as cell shape to that typical of some transcription factors, which are less functionally predictable when altered. The latter may be expressed developmentally, in compartmentalized manner, or only intermittently and yet exert vastly ramified influences sometimes circumscribed only to select species. We also argue that genetic diseases may steer the organism toward often poorly understood biological end points and co-opt multiple processes into hardly modifiable biology. Addition or modification of genes to approximate a normal state not previously experienced by the organism may lead to further aberration due to extraneous interference with the native biology of the disease state. Therefore, an understanding as perspicuous as possible of gene function, regulation, modifiability, and biological directionality down to seemingly minute but disease-relevant consequences is a prerequisite to intervention. Although we provide some groundwork steps to such an understanding, this may occasionally prove unattainable.

Evaluation of Radiotherapy Dose and Survival Outcomes for Teenagers, and Young Adults with Nasopharyngeal Carcinoma in UK and Ireland

PURPOSE/OBJECTIVE(S)

Nasopharyngeal carcinoma (NPC) follows a bimodal distribution with a smaller incidence peak in teenagers and young adults (TYAs). In TYAs, an over-whelming proportion are associated with Epstein-Barr virus (EBV). We have evaluated the variation in TYA NPC practice patterns across the UK and Ireland, along with survival outcomes.

MATERIALS/METHODS

We performed a multicenter, observational cohort study, of patients aged 13-25 years, with histologically confirmed NPC, treated between the years 2002-2022. An initial expression of interest was sent to selected centers treating H&N patients in the UK and Ireland. For analysis, patients were assessed based on total prescribed dose, with a cut off for low dose (LD) (≤61.2Gy) versus a high dose (HD)(>61.2Gy).

RESULTS

Ninety-five patients, from 9 centers, were eligible for inclusion. Patient demographics are shown in table1. At a median follow up of 45 months (IQR 23-111), 3-year overall survival (OS) was 98% (95% CI 93%-100%) with LD versus 91% (95% CI 83%-99%) with HD (Hazard ratio (HR) = 3.0; 95% CI 0.3-27, p = 0.3). 3-year progression free survival (PFS) was 84% (95% CI 71%-97%) with LD versus 83% (95% CI 72%-94%) with HD (HR 1.3; 95% CI 0.4-4.0, p = 0.6), and 5-year PFS was 84% (95% CI 71%-97%) with LD versus 83% (95% CI 72%-94%) with HD (HR 1.3; 95% CI 0.4-4.0, p = 0.6). Incidence of distant metastasis (DM) was 9.9%. 2 patients (6%) with T3-T4 tumors, treated with LD, had locoregional failure (LRF) compared to 1 patient (3%) treated with HD.

CONCLUSION

We have demonstrated excellent survival outcomes for the UK & Ireland TYA NPC patients. As the majority of cases in this age group have EBV+ NPC, with survival similar between LD and HD protocols, we propose that pediatric protocols, with lower radiotherapy doses should be considered for all TYA NPC, with the aim of reducing late effects. Additional analysis to better understand the impact of heterogeneity between both groups, including choice of protocol, induction and adjuvant treatment will follow this study. Prospective evaluation, as part of an international collaboration, is required to optimize the management strategy for this rare cohort of patients.

A Multicenter Study of Clinician and Patient Reported Acute and Late Toxicity after Radical (Chemo)Radiotherapy for Non-Endemic Nasopharyngeal Cancer

PURPOSE/OBJECTIVE(S)

Curative (chemo)radiotherapy ((CT)RT) for Nasopharyngeal cancers (NPC) achieves excellent disease control but is associated with significant late toxicities despite modern treatment delivery. Contemporary late toxicity data, including patient reported outcomes (PROs), is limited in the non-endemic population; we present a large contemporary series of toxicity outcomes and late PROs following treatment of non-endemic NPC.

MATERIALS/METHODS

Adult patients completing radical (CT)RT for primary NPC between February 2016 and 2020 at 7 large UK cancer centers were identified on institutional databases. Patients were excluded if they had prior head and neck cancer or prior therapeutic head and neck surgery (except neck dissection). Patients with an active other cancer were excluded from PRO assessment. Demographic, treatment, acute toxicity and outcome data were collected retrospectively from patient records. Disease-free patients were invited to complete an M.D. Anderson Dysphagia Index (MDADI) and University of Washington (UoW) Quality of Life (QoL) PROs questionnaires.

RESULTS

A total of 180 eligible patients were identified: 68% male, median age 54 years, 11% ≥70 years. EBV status was positive in 61% (unknown 12%). Patients had stage I (5%), II (22%), III (37%), IV (36%) disease; 95% were performance status ≤1 at baseline. Median follow-up was 31.2 months (range 0-68). A total of 54% received 70Gy in 33-35# and 43% received 65-66 Gy in 30-33#. 66% received induction and 65% received concurrent chemotherapy. 9.5% had residual disease at the first follow-up scan. Subsequent locoregional or distant recurrence occurred in 5% and 12% respectively. At last assessment, 84% patients were alive, 16% had died (of which 70% had active disease). Acute treatment toxicity included: 63% of patients required enteral support (median duration 98 days) with 9% a feeding tube at 1 year post treatment. 18% G3 dermatitis, 53% G3 mucositis. 82% requiring opioids and 40% admitted for symptom management. 90 patients completed the PROs (76% response rate) at a median of 37.8 months post treatment (Table 1). These demonstrate significant QoL detriment: 28% report significant pain, 24% require regular analgesia, and 59% report significant impact on daily activity. This was found to persist at different timepoints (not shown).

CONCLUSION

Excellent cancer survival outcomes are seen in a non-selected, non-endemic NPC population. However significant acute and late toxicity following radical treatment is identified which can profoundly negatively impact QoL in a relatively young cohort. This highlights the importance of ongoing efforts to reduce toxicity and supports the prospective evaluation of potential toxicity sparing technologies, such as proton beam radiotherapy.

Silvio Weidmann: laying the foundations for unravelling the mechanism of heart rhythm

Silvio Weidmann laid the basis of cardiac electrophysiology and was the forerunner in the search for mechanisms governing the electrical activity of the heart in his legendary first studies of Purkinje fibres in the 1950s. His work was the cornerstone of research in this field for many generations, and countless cardiologists and electrophysiologists have based their studies on the knowledge generated by Weidmann's pioneering data. This review summarizes his key contributions from the first intracellular recordings of cardiac membrane potentials in 1949 to the publication of his monograph in 1956. That summary is followed by an imagined dialogue between the authors and Silvio Weidmann himself, in the format of a one-act play. Both of us have such good recollections of our real-life conversations with Silvio Weidmann that we decided we could achieve a better feel for the history and issues by using a dialogue format. We hope that, in that way, we may transmit the character of Silvio Weidmann better for those readers who will not have known him personally. Silvio Weidmann was an extraordinarily sensitive and conversational person as well as a great scientist, and we feel it is worth the effort to convey that fact here. This article is part of the theme issue 'The heartbeat: its molecular basis and physiological mechanisms'.

Gregor Mendel at the source of genetics and systems biology

Gregor Mendel is generally presented as the ‘ignored and solitary founder of genetics’. This Moravian friar would have worked in strict isolation on the heredity of peas in the garden of his monastery, and his experiments would have been ignored by his contemporaries, before being ‘rediscovered’ independently by three botanists in 1900, 34 years after their publication. Historians have contributed to replace the genesis of Mendel’s work in the context of his time, questioning the mythical image that prevailed in academic circles and the public perception. This paper recalls that Mendel benefitted from a very favourable context for the development of his experiments at St Thomas Monastery in Brno and was not isolated from the scientific community of his time. Although the notions on which his work was based were already present in scientific publications, this does not diminish the importance of Mendel’s contribution to the development of modern biology. We provide a detailed analysis of the results of his experiments on the development of hybrid plants that he presented in two lectures at the Brno Society of Natural History in 1865, demonstrating that beyond his major contribution to the foundation of genetics, Mendel was one of the pioneers of systems biology.

Modern physiology vindicates Darwin's Dream

New Findings

What is the topic of this review?

Revisiting the 2013 article ‘Physiology is rocking the foundations of evolutionary biology’.

What advances does it highlight?

The discovery that the genome is not isolated from the soma and the environment, and that there is no barrier preventing somatic characteristics being transmitted to the germline, means that Darwin's pangenetic ideas become relevant again.

Abstract

Charles Darwin spent the last decade of his life collaborating with physiologists in search of the biological processes of evolution. He viewed physiology as the way forward in answering fundamental questions about inheritance, acquired characteristics, and the mechanisms by which organisms could achieve their ends and survival. He collaborated with 19th century physiologists, notably John Burdon‐Sanderson and George Romanes, in his search for the mechanisms of transgenerational inheritance. The discovery that the genome is not isolated from the soma and the environment, and that there is no barrier preventing somatic characteristics being transmitted to the germline, means that Darwin's pangenetic ideas become relevant again. It is time for 21st century physiology to come to the rescue of evolutionary biology. This article outlines research lines by which this could be achieved.

Review of historic article: Skou 1964 enzymatic aspects of active linked transport of Na+ and K+ through the cell membrane. Progress in Biophysics and Molecular Biology, 14, 133-166

In this historic article we witness the author's own account of his great discovery: the nature and location of the enzyme system enabling sodium-potassium exchange across membranes in living cells, particularly nerve cells. That discovery has stood the test of time. active ion transport of sodium and potassium ions through cell membranes is ubiquitous.

Review of historic article: Ebashi, S & Endo, M. 1968 Calcium Ion and Muscle Contraction. Progress in Biophysics and Molecular Biology, 18, 123-183

The 1968 review article on Calcium ion and muscle contraction by Setsuro Ebashi and Makoto Endo is one of the highest cited in the journal since it was required reading in the early days of understanding what triggers contraction of the myofilaments. It correctly identified the major steps in excitation-contraction coupling and still inspires mathematical models of muscle activity today. It also successfully identified the role of troponin.

Review of historic article: Huxley 1957 Muscle Structure and theories of contraction. Progress in Biophysics and biophysical chemistry, 7, 255-318

The article by Andrew Huxley in this journal in 1957, "Muscle Structure and theories of Contraction" is much more than a standard review of a field. It is itself a major theoretical modelling achievement: the first mathematical model of the contractile process in skeletal muscle. That model was based on careful microscopic analysis of the striation patterns in skeletal muscles. Cited 4456 times, it holds the record for this journal.

Review of historic article: Butler, J.A.V., Johns, E.W. and Philips, D. M. P. 1968. Recent investigations on histones and their functions. Progress in Biophysics and molecular biology, 18, 209-244

This Historic Article was based on pioneering work by the laboratory of the Founding Editor of the journal to characterise the different forms of histones in the nucleus and their relationship with DNA. The classification determined in 1968 bears strong relationship to that known today. Most importantly, the work clarified that the inhibitory effect of histones on DNA is a general one and would not explain the subsequent differentiation of cells during development in multicellular organisms. Extensive work on the amino acids in histones leads to the understanding that negatively charged DNA naturally attaches itself to positively charged histones.

A Quantitative Systems Pharmacology Perspective on the Importance of Parameter Identifiability

There is an inherent tension in Quantitative Systems Pharmacology (QSP) between the need to incorporate mathematical descriptions of complex physiology and drug targets with the necessity of developing robust, predictive and well-constrained models. In addition to this, there is no “gold standard” for model development and assessment in QSP. Moreover, there can be confusion over terminology such as model and parameter identifiability; complex and simple models; virtual populations; and other concepts, which leads to potential miscommunication and misapplication of methodologies within modeling communities, both the QSP community and related disciplines. This perspective article highlights the pros and cons of using simple (often identifiable) vs. complex (more physiologically detailed but often non-identifiable) models, as well as aspects of parameter identifiability, sensitivity and inference methodologies for model development and analysis. The paper distills the central themes of the issue of identifiability and optimal model size and discusses open challenges.

Origins and demise of selfish gene theory

The idea of The Selfish Gene, first published in 1976, grew out of the Modern Synthesis of evolutionary biology formulated by Julian Huxley in 1942, and more specifically from George Williams' Adaptation and Natu - ral Selection in 1966. It presents a severely narrowed down version of Huxley's synthesis, which developed in the 1960s following the formulation of the Cen tral Dogma of molecular biology by Francis Crick. The idea rests on three assumptions: the isolation of the genome from any influences by the soma and its development in interaction with the environment (the Weis - mann Barrier), one-way causation from DNA to proteins (The Central Dogma), and the autoreplication of DNA (Schrödinger's aperiodic crystal). All three of these assumptions have now been shown to be incorrect. The 'replicator' (DNA) is not independent of the 'vehicle', the organism itself, so that The Selfish Gene can no longer be regarded as a valid scientific hypothesis.

Biological relativity revisited: the pre-eminent role of values

Multilevel interpretations of development and evolution take to heart the contextual nature of both those processes, and so necessarily assume top-down causation occurs, right down to the physics level. In this article we revisit the Principle of Biological Relativity proposed by Noble in 2012, where all emergent levels of organisation are equally causally valid. While this is true in general for physical interactions between levels, we argue that in the case of conscious organisms making rational choices, there is indeed a preferred causal origin - namely the overall embracing influence of meaning and values. This is the opposite of what is suggested by a reductionist viewpoint, where it is the bottom-most physical level that is stated to be causally preferred (by some physicists), or the genetic level (by some evolutionary theorists). Charles Darwin was therefore correct to distinguish between Artificial (conscious) Selection, where values enter, and Natural Selection. The Modern Synthesis was wrong to exclude Darwin's distinction.

Cellular Darwinism: Regulatory networks, stochasticity, and selection in cancer development

There are strong parallels between the evolutionary origin of species within populations of organisms and new concepts for the origin of cancers within cell populations in the tissues of the body. The analogy is that cancers can be regarded as a new somatic species developing within the host organism. In both cases, understanding the processes involved requires a multi-scale analysis, including higher-level control of genetic and epigenetic changes. A key to developing successful therapeutic strategies will be to identify the processes that control heterogeneity in tissues. These include processes outside the currently dominant theory of evolution, i.e. the Modern Synthesis. Specifically, organisms can partially direct both genetic and epigenetic changes through the harnessing of chance. The loci and rates of mutation and of genome reorganisation are forms of targeted functional reorganisation of genomes. They are more likely to result in functional reorganisations compared to the slow accumulation of point mutations.

Effects of Natura 2000 on nontarget bird and butterfly species based on citizen science data

The European Union's Natura 2000 (N2000) is among the largest international networks of protected areas. One of its aims is to secure the status of a predetermined set of (targeted) bird and butterfly species. However, nontarget species may also benefit from N2000. We evaluated how the terrestrial component of this network affects the abundance of nontargeted, more common bird and butterfly species based on data from long-term volunteer-based monitoring programs in 9602 sites for birds and 2001 sites for butterflies. In almost half of the 155 bird species assessed, and particularly among woodland specialists, abundance increased (slope estimates ranged from 0.101 [SD 0.042] to 3.51 [SD 1.30]) as the proportion of landscape covered by N2000 sites increased. This positive relationship existed for 27 of the 104 butterfly species (estimates ranged from 0.382 [SD 0.163] to 4.28 [SD 0.768]), although most butterflies were generalists. For most species, when land-cover covariates were accounted for these positive relationships were not evident, meaning land cover may be a determinant of positive effects of the N2000 network. The increase in abundance as N2000 coverage increased correlated with the specialization index for birds, but not for butterflies. Although the N2000 network supports high abundance of a large spectrum of species, the low number of specialist butterflies with a positive association with the N2000 network shows the need to improve the habitat quality of N2000 sites that could harbor open-land butterfly specialists. For a better understanding of the processes involved, we advocate for standardized collection of data at N2000 sites.

Investigation of the Cellular Pharmacological Mechanism and Clinical Evidence of the Multi-Herbal Antiarrhythmic Chinese Medicine Xin Su Ning

Xin Su Ning (XSN), a China patented and certified multi-herbal medicine, has been available in China since 2005 for treating cardiac ventricular arrhythmia including arrhythmia induced by ischemic heart diseases and viral myocarditis, without adverse reactions being reported. It is vitally important to discover pharmacologically how XSN as a multicomponent medicine exerts its clinical efficacy, and whether the therapeutic effect of XSN can be verified by standard clinical trial studies. In this paper we report our discoveries in a cellular electrophysiological study and in a three-armed, randomized, double-blind, placebo-controlled, parallel-group, multicenter trial. Conventional electrophysiological techniques were used to study the cellular antiarrhythmic mechanism of XSN. Data was then modeled with computational simulation of human action potential (AP) of the cardiac ventricular myocytes. The clinical trial was conducted with a total of 861 eligible participants randomly assigned in a ratio of 2:2:1 to receive XSN, mexiletine, or the placebo for 4 weeks. The primary and secondary endpoint was the change of premature ventricular contraction (PVC) counts and PVC-related symptoms, respectively. This trial was registered in the Chinese Clinical Trial Register Center (ChiCTR-TRC-14004180). We found that XSN prolonged AP duration of the ventricular myocytes in a dose-dependent, reversible manner and blocked potassium channels. Patients in XSN group exhibited significant total effective responses in the reduction of PVCs compared to those in the placebo group (65.85% vs. 27.27%, P < 0.0001). No severe adverse effects attributable to XSN were observed. In conclusion, XSN is an effective multicomponent antiarrhythmic medicine to treat PVC without adverse effect in patients, which is convincingly supported by its class I & III pharmacological antiarrhythmic mechanism of blocking hERG potassium channels and hNaV1.5 sodium channel reported in our earlier publication and prolongs AP duration both in ventricular myocytes and with computational simulation of human AP presented in this report.

Biological Relativity Requires Circular Causality but Not Symmetry of Causation: So, Where, What and When Are the Boundaries?

Since the Principle of Biological Relativity was formulated and developed there have been many implementations in a wide range of biological fields. The purpose of this article is to assess the status of the applications of the principle and to clarify some misunderstandings. The principle requires circular causality between levels of organization. But the forms of causality are also necessarily different. They contribute in asymmetric ways. Upward causation can be represented by the differential or similar equations describing the mechanics of lower level processes. Downward causation is then best represented as determining initial and boundary conditions. The questions tackled in this article are: (1) where and when do these boundaries exist? and (2) how do they convey the influences between levels? We show that not all boundary conditions arise from higher-level organization. It is important to distinguish those that do from those that don't. Both forms play functional roles in organisms, particularly in their responses to novel challenges. The forms of causation also change according to the levels concerned. These principles are illustrated with specific examples.