Rosen's (M,R) system in Unified Modelling Language

A biochemically-realisable relational model of the self-manufacturing cell

As shown by Hofmeyr, the processes in the living cell can be divided into three classes of efficient causes that produce each other, so making the cell closed to efficient causation, the hallmark of an organism. They are the enzyme catalysts of covalent metabolic chemistry, the intracellular milieu that drives the supramolecular processes of chaperone-assisted folding and self-assembly of polypeptides and nucleic acids into functional catalysts and transporters, and the membrane transporters that maintain the intracellular milieu, in particular its electrolyte composition. Each class of efficient cause can be modelled as a relational diagram in the form of a mapping in graph-theoretic form, and a minimal model of a self-manufacturing system that is closed to efficient causation can be constructed from these three mappings using the formalism of relational biology. This fabrication-assembly or (F,A)-system serves as an alternative to Robert Rosen's replicative metabolism-repair or (M,R)-system, which has been notoriously problematic to realise in terms of real biochemical processes. A key feature of the model is the explicit incorporation of formal cause, which arrests the infinite regress that plagues all relational models of the cell. The (F,A)-system is extended into a detailed relational model of the self-manufacturing cell that has a clear biochemical realisation. This (F,A) cell model allows the interpretation and visualisation of concepts such as the metabolism and repair components of Rosen's (M,R)-system, John von Neumann's universal constructor, Howard Pattee's symbol-function split via the symbol-folding transformation, Marcello Barbieri's genotype-ribotype-phenotype ontology, and Tibor Gánti's chemoton.

Individuation and the Organization in Complex Living Ecosystem: Recursive Integration and Self-assertion by Holon-Lymphocytes

Individuation and organization in complex living multi-level ecosystem occurs as dynamical processes from early ontogeny. The notion of living "holon" displaying dynamic self-assertion and integration is used here to explain the ecosystems dynamic processes. The update of the living holon state according to the continuous change of the dynamic system allows for its viability. This is interpreted as adaptation, selection and organization by the human that observes the system a posteriori from its level. Our model concerns the complex dynamics of the adaptive immune system, integrating holon-lymphocytes that collectively preserve the identity and integrity of the organism. Each lymphocyte individualizes as a dynamic holon-lymphocyte, with somatic gene individuation leading to an individual, singular antigen immunoreceptor type, promoting the self-assertion. In turn, the "Immunoception" allows for perception of the environmental antigenic context, thus integration of the holon in its environment. The self-assertion/integration of holon-lymphocyte starts from fetal stages and is influenced by mother Lamarckian acquired historicity transmissions, a requisite for the integrity of the holobiont-organism. We propose a dynamic model of the perception by holon-lymphocyte, and at the supra-clonal level of the immune system functions that sustain the identity and integrity of the holon-holobiont organism.

Rethinking gamete donor care: A satisfaction survey of egg and sperm donors in the UK

OBJECTIVE

Despite poor clinic communication and staff treatment being reported by donors, high rates of overall satisfaction are still reported in surveys. This study will evaluate the importance of communication and interaction between donors and fertility clinic staff in gamete donor care.

METHODS

We report on 120 egg and sperm donors' responses to a UK-wide online satisfaction survey. The survey focused on donors' interactions with fertility clinic staff pre-, during, and post- donation. Basic cross-tabulation was performed on the data using online survey software. Textual data was read and extracts identified, which illustrated and expanded on the findings from the numerical data. Diagrammatic modeling was also utilised to analyse the textual data, with particular focus to relationships between the donors and clinic staff, the main activities within the gamete donation process, and how these activities may affect donor satisfaction with the gamete donation process.

RESULTS

Donors expressed concern for the infertile couple and the resulting child; conveyed frustration at not receiving information on the expenses they could claim; felt lost in the system regarding the ease of making clinic appointments, and once made they were routinely not seen on time for these appointments. Donors also negatively commented on aftercare, the location and condition of the donation room, and information on contraception. In addition, Ovarian Hyperstimulation Syndrome was frequently reported, with these egg donors believing that clinic staff were not concerned with their physical or emotional well-being, but were instead disproportionately focused on extracting the eggs.

CONCLUSIONS

The multifaceted notion of donors highlights the complexity inherent to the gamete donation process, which comprises various aspects of uncertainty in the donation system, and ambiguity in the donation process. Categorising donors as Altruist, Customer, and Patient, conveys the particular importance of staff communication and treatment in donor care. These categories are not mutually exclusive however, in that an individual donor may experience more than one of these perspectives during the course of their gamete donation journey. Finally, there were a number of exemplar cases, where donors reported high satisfaction throughout, and these correlated with them being given a single point of contact at the clinic. Subject to resource constraints, we suggest that this practice should be implemented throughout clinics in the UK, so that donors have access to dedicated clinic staff who not only support them emotionally and physically throughout the gamete donation process, but also ensure that communication is open, clear, timely, and consistent.

Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems

Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model. We present a domain model of the IL-1 stimulated NF-κB signalling pathway, which unambiguously defines the spatial, temporal and stochastic requirements for our future computational model. Through the development of this model, we observe that, in isolation, UML is not sufficient for the purpose of creating a domain model, and that a number of descriptive and multivariate statistical techniques provide complementary perspectives, in particular when modelling the heterogeneity of dynamics at the single-cell level. We believe this approach of using UML to define the structure and interactions within a complex system, along with statistics to define the stochastic and dynamic nature of complex systems, is crucial for ensuring that conceptual models of complex dynamical biosystems, which are developed using UML, are fit for purpose, and unambiguously define the functional requirements for the resultant computational model.