Mechanism, autonomy and biological explanation

The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual mechanisms, while the autonomy approach can ground itself in biological research into how the actual components constituting an autonomous system interact and contribute in different ways to realize and maintain the system. To press the case that these two traditions should be constructively integrated we describe how three recent developments in the autonomy tradition together provide a bridge between the two traditions: (1) a framework of work and constraints, (2) a conception of function grounded in the organization of an autonomous system, and (3) a focus on control.

Forms as Forces: The Causal Regime of Morphology in Biology

Traditionally, morphology is seen merely as an auxiliary subdiscipline of biology and other fields. Allegedly, it does not provide explanations for phenomena but merely describes forms as a preliminary step in their analysis. Here, the view is defended that forms, and hence morphology, can also take over an important explanatory function and even, ultimately, constitute the explanatory level fundamental to biology as a distinct science. According to this thesis, the form of organisms and their parts provide the only specifically biological causal factors. Nothing but the form, the specific spatial arrangement of matter, determines the peculiarity of organisms’ ways of being. Therefore, biological explanation must start from specific structures. These structures provide the respective boundary conditions for harnessing the general laws of nature, thus determining their trajectory. Ultimately, then, forms play the most fundamental explanatory role in biology.

Length Biases in Single-Cell RNA Sequencing of pre-mRNA

Single-molecule pre-mRNA and mRNA sequencing data can be modeled and analyzed using the Markov chain formalism to yield genome-wide insights into transcription. However, quantitative inference with such data requires careful assessment and understanding of noise sources. We find that long pre-mRNA transcripts are over-represented in sequencing data, and explore the mechanistic implications. A biological explanation for this phenomenon within our modeling framework requires unrealistic transcriptional parameters, leading us to posit a length-based model of capture bias. We provide solutions for this model, and use them to find concordant and mechanistically plausible parameter trends across data from multiple single-cell RNA-seq experiments in several species.

Ectogenesis and Representations of Future Motherings in Helen Sedgwick’s The Growing Season

After the boom of feminist science fiction in the 1970s, many such novels have tackled the different sociocultural understandings of gender and sexual reproduction. Conventionally, patriarchal thinking tends to posit a biological explanation for gender inequality: women are supposed to be child bearers and the primary caregivers, whereas men should provide for the family through their work. However, if men could share procreation, would these views change? A recent work of fiction exploring this question from multiple perspectives is Helen Sedgwick’s The Growing Season (2017), a novel that presents a near future in which babies can be grown in artificial wombs that can be carried around. As an analysis of the novel will show, The Growing Season creatively explores the existing tensions among contemporary understandings of motherhood and feminism(s), as well as developments in reproductive biotechnology, through the different perspectives offered by the heterodiegetic third-person narration and multiple focalisation. Ultimately, the voices of the different characters in the novel convey a polyhedral vision of possible future feminist motherhood(s) where ideas of personal freedom and codependency are radically reconceptualised—a rethinking that becomes especially important nowadays, for the biotechnological elements of this fictional dystopia are already a reality.

Mast Cell Sensitization as a Plausible and Researchable Mechanism for Chemical Intolerance

Background Worldwide observations provide evidence for a two-stage disease process called Toxicant-Induced Loss of Tolerance (TILT), described in this journal in the first of two related papers. The disease process is initiated by a major exposure event, or a series of lower level exposures (Stage I, Initiation). Subsequently, affected individuals report that common chemical inhalants, foods, and drugs trigger multisystem symptoms (Stage II, Triggering). Given that foods and drugs also are comprised of chemicals, we refer to these intolerances simply as “chemical intolerance” (CI). In this second, companion paper we propose mast cell sensitization and mediator release as a plausible and researchable biological explanation for TILT. Methods Using the Quick Environmental Exposure and Sensitivity Inventory (QEESI), we compared patients diagnosed with mast cell activation syndrome (MCAS) (n = 147) to individuals who reported chemical intolerances following various exposures (n = 345), and to controls (n = 76). We compared QEESI scores using ANOVA across groups. Clinical scores for the MCAS patient group were used to predict CI status using logistic regression. Results As the likelihood of patients’ having CI increased, their likelihood of having MCAS similarly increased, to a near-perfect correspondence at the high ends of the QEESI and clinical MCAS scores. Symptom patterns were near-identical for CI and MCAS groups. Conclusion The close correspondence between QEESI scores for MCAS and TILT patients supports mast cell sensitization and mediator release as a plausible biological mechanism underlying both conditions, with implications for medicine, environmental health, and regulatory toxicology.

The Scientific Images of the Axolotl by José María Velasco and Their Role in Nineteenth-Century Evolutionary Thinking

This paper examines the study and images of the Mexican amphibian axolotl published by the Mexican landscape painter José María Velasco in 1879. Soon thereafter Velasco encountered the study of the same amphibian written by the German Neo-Darwinist August Weismann. Velasco disputed Weismann’s evolutionary views and defended his own observations. Through an analysis of Velasco’s images, I argue that their aesthetic features were strategic to developing a biological explanation of the creature’s development. This interaction between image and scientific explanation sheds light on the significance of visual objects within the expansion of Darwinism in the late nineteenth century, and within the development of laboratory research. I argue that changes in global scientific networks and the expansion of new techniques of research necessitate a rethinking of the nexus between observation and the scientific image.

ACE2 polymorphisms as potential players in COVID-19 outcome

The clinical condition COVID-19, caused by SARS-CoV-2, was declared a pandemic by the WHO in March 2020. Currently, there are more than 5 million cases worldwide, and the pandemic has increased exponentially in many countries, with different incidences and death rates among regions/ethnicities and, intriguingly, between sexes. In addition to the many factors that can influence these discrepancies, we suggest a biological aspect, the genetic variation at the viral S protein receptor in human cells, ACE2 (angiotensin I-converting enzyme 2), which may contribute to the worse clinical outcome in males and in some regions worldwide. We performed exomics analysis in native and admixed South American populations, and we also conducted in silico genomics databank investigations in populations from other continents. Interestingly, at least ten polymorphisms in coding, noncoding and regulatory sites were found that can shed light on this issue and offer a plausible biological explanation for these epidemiological differences. In conclusion, there are ACE2 polymorphisms that could influence epidemiological discrepancies observed among ancestry and, moreover, between sexes.

Plant functional types determine how close postfire seedlings are from their parents in a species-rich shrubland

Background and Aims Fine-scale spatial patterns of the seedlings of co-occurring species reveal the relative success of reproduction and dispersal and may help interpret coexistence patterns of adult plants. To understand whether postfire community dynamics are controlled by mathematical, biological or environmental factors, we documented seedling–adult (putative parent) distances for a range of co-occurring species. We hypothesized that nearest-seedling-to-adult distances should be a function of the distance between the closest conspecific seedlings, closest inter-adult distances and seedling-to-parent ratios, and also that these should scale up in a consistent way from all individuals, to within and between species and finally between functional types (FTs). Methods We assessed seedling–adult, seedling–seedling and adult–adult distances for 19 co-occurring shrub species 10 months after fire in a species-rich shrubland in south-western Australia. Species were categorized into 2 × 2 FTs: those that are killed by fire [non-(re)sprouters] vs. those that survive (resprouters) in nine taxonomically matched pairs, and those that disperse their seeds prefire (geosporous) vs. those that disperse their seeds postfire (serotinous). Key Results For the total data set and means for all species, seedling–adult distance was essentially a mathematical phenomenon, and correlated positively with seedling–seedling distance and adult–adult distance, and inversely with seedlings per adult. Among the four FTs, seedling–adult distance was shortest for geosporous non-sprouters and widest for serotinous resprouters. Why adults that produce few seedlings (resprouters) should be further away from them defies a simple mathematical or biological explanation at present. Ecologically, however, it is adaptive: the closest seedling was usually under the (now incinerated) parent crown of non-sprouters whereas those of resprouters were on average four times further away. Conclusions Our study highlights the value of recognizing four reproductive syndromes within fire-prone vegetation, and shows how these are characterized by marked differences in their seedling–adult spatial relations that serve to enhance biodiversity of the community.