Bartlomiej Swiatczak

University of Science and Technology of China | USTC · Department of History of Science and Scientific Archaeology

Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for unde...

Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which...

The extent to which normal (nonmalignant) cells of the body can evolve through mutation and selection during the lifetime of the organism has been a major unresolved issue in evolutionary and developmental studies. On the one hand, stable mul-ticellular individuality seems to depend on genetic homogeneity and suppression of evolutionary conflicts a...

To enable microbial colonisation of the gut mucosa, the intestinal immune system must not only react to danger signals but also recognize cues that indicate safety. Safety recognition, paradoxically, is mediated by the same environmental sensors that are involved in signalling danger. Indeed, in addition to their well established role in inducing i...

Originating in the work of Ernst Haeckel and Wilhelm Preyer, and advanced by a Prussian embryologist, Wilhelm Roux, the idea of struggle for existence between body parts helped to establish a framework, in which population cell dynamics rather than a predefined harmony guides adaptive changes in an organism. Intended to provide a causal-mechanical...

While the first-person style of philosophising has a long tradition dating back to Plato and Socrates, it has been almost completely abandoned in modern times, as scholars tend to present their philosophical ideas in a matter-of-fact manner, omitting (or concealing) possible biases, personal preferences, and dispositions. That such an approach give...

Long noncoding RNAs (lncRNAs) possess the potential for therapeutic targeting to treat many disorders, including cancers. Several RNA-based therapeutics (ASOs and small interfering RNAs) have gained FDA approval over the past decade. And with their potent effects, lncRNA-based therapeutics are of emerging significance. One important lncRNA target i...

Central to vaccination-induced responses, antibodies are suggested by Vaz to operate as observer-dependent entities that owe their status to categorization schemes of immunologists. Inspired by color research by Maturana, he argues that antibodies should be distinguished from immunoglobulins, which unlike the former can be considered as constituent...

Apparent parallels between natural language and biological sequence have led to a recent surge in the application of deep language models (LMs) to the analysis of antibody and other biological sequences. However, a lack of a rigorous linguistic formalization of biological sequence languages, which would define basic components, such as lexicon (i.e...

There is a deep-seated neopositivist view which regards the language of science as a neutral medium of communication, radically different from indirect symbolic forms of discourse characteristic of arts and humanities. But naturalists, like poets and social scientists, also draw on the dominant images in their culture to organize their thoughts and...

The fight to find effective, long-lasting treatments for cancer has led many researchers to consider protein degrading entities. Recent developments in PROteolysis TArgeting Chimeras (PROTACs) have signified their potential as possible cancer therapies. PROTACs are small molecule, protein degraders that function by hijacking the built-in Ubiquitin-...

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely blackbox models and thus challenging to interpret, current protein LM approaches do not contribute to a fundamental understanding of sequence-function mappings, hindering rule-based biothe...

In search of organizing principles of the immune system William E. Paul: Immunity. Baltimore: John Hopkins University Press, 2015, 289pp, $29.95 China, Hefei, China Immunity by William Paul is an overview of fundamental principles of immunology and their experimental basis. The book includes not only well- established facts about the immune system...

It has long been taken for granted that the immune system’s capacity to protect an individual from infection and disease depends on the power of the system to distinguish between self and nonself. However, accumulating data have undermined this fundamental concept. Evidence against the self/nonself discrimination model left researchers in need of a...

The idea that the immune system distinguishes between self and non-self was one of the central assumptions of immunology in the second half of 20th century. This idea influenced experimental design and data interpretation. However, in the face of new evidence there is a need for a new conceptual framework in immunology.

Coordination of immune responses in the gut is a complex task. In order to fight pathogens and maintain a defined population of commensal microbes, the mucosal immune system has to coordinate information from the external (luminal) and internal (abluminal) environment and respond accordingly. Dendritic cells (DCs) are crucial cell types involved in...

The immune system, to protect the body, must discriminate between the pathogenic and non-pathogenic microbes and respond to them in different ways. How the mucosal immune system manages to make this distinction is poorly understood. We suggest here that the distinction between pathogenic and non-pathogenic microbes is made by an integrated system r...

One of the fundamental questions of life sciences is one of whether there are genuinely random biological processes. An affirmative or negative answer to this question may have important methodological consequences. It appears that a number of biological processes are explicitly classified as random. One of them is the so-called somatic hypermutati...

Advocates of the computational theory of mind claim that the mind is a computer whose operations can be implemented by various computational systems. According to these philosophers, the mind is multiply realisable because—as they claim—thinking involves the manipulation of syntactically structured mental representations. Since syntactically struct...