Writing

Thinking in public

Short essays, technical notes, and literature reflections — a place to test an idea, work through a graph or statistics problem, or summarize a paper. Less news, more notebook.

A Map of Immunological Theories

immunological theories
essay
idiotypy
systems immunology

Clonal selection, Two Signal Theory - T help, Two Signal Theory - APC, Functional Recognition, Stranger (PRR) / Danger Theories, Continuity Theory, Idiotypic Netowrks, Symmetrical Network, Coutinho’s Completeness, Irun Cohen’s Cognitive Paradigm (homunculus)

Jul 9, 2026

Does evolution ‘care’ about idiotypy?

repertoire physics
essay
idiotypy
systems immunology

Is there a functional idiotypic network? Why do idiotypic antobdies exist? What is the role of anti-idiotypic antibodies in evolution?

Jul 4, 2026

The space of antibody reactivities modelled by mimotope libraries - IgOme

antibody repertoire
mimotopes
essay
space of reactivities

Antibody repertoires can be studied by BCR sequencing or by selection of sets of random peptides - IgOme or phage immunoprecipitation sequencing (PhIP-Seq).

Jun 29, 2026

Antibody specificity is actually a fluid concept

specificity
essay

Treating broad binding as measurement error throws away signal, antibody specificity is conditional.

Jun 28, 2026

Reading a reactivity graph

graphs
IgM
note

The cross-reactivity landscape can be studied using both IgOme libraries and high-throughput binding assays on microarrays.

Jun 27, 2026

Specificity is a shape, not a switch

specificity
statistical mechanics
antibody binding
essay

Why the lock-and-key picture under-describes real antibodies, and what describing specificity as the shape of an affinity distribution over epitope space buys us — with the binding physics made explicit.

May 15, 2026
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