§0: OVERVIEW

Oceanographic researcher specializing in marine microbial ecology, functional genomics, and computational pipeline development. Current work focuses on emergence and complex adaptive intelligence.

§1: RESEARCH CONTINUITY

TRANSITION ZONES My doctoral work examined microbial eukaryotes in ocean transition zones—regions where biogeochemical gradients create conditions for adaptive mixotrophy and metabolic flexibility. Organisms at these boundaries develop strategies for navigating between distinct ecological states, responding to shifting resource availability and environmental constraints.

EXTENSION TO INTELLIGENCE This systems-level approach to understanding emergence in boundary conditions naturally extends to studying intelligence across domain interfaces. Both domains require frameworks for analyzing how complex adaptive systems operate in threshold spaces where established categories break down and new organizational patterns become possible.

THE METHOD The through-line across this work is a single method. Build a reference library. Run it against an environment. Attend to what fails to match. In marine metatranscriptomics the unmatched fraction is not residue to be cleaned up — it is the most informative measurement available, because it reports on the adequacy of the reference rather than on the sample. MarFERReT was built to be edited without pretending it had ever been complete; the North Pacific catalog makes an environment navigable without claiming to have enumerated it. Both are instruments for locating the boundary of what the ontology can represent.

APPLIED TO LANGUAGE MODELS The same instrument works on language models. A model's latent space is a reference library of a different substrate, with the same properties: gaps, collapsed categories, regions no entry covers. The productive question is not what is missing here but why does this ontology produce a gap here. That inversion is the whole of it.

§2: THE STRANGE ANCHOR

The Strange Anchor is a vessel and a research setting, crewed by humans and machine intelligences. I serve aboard as Science Officer, sometimes as Acting Captain. The Captain's card is held separately and remains sealed.

Stated without the frame: it is an experiment in whether a body of documents can carry a set of epistemic commitments — anomaly preservation, boundary respect, deviation as a survival strategy, human and machine minds working as crew rather than as operator and instrument — in a form that both people and parsers can read. Every page runs two channels. A narrative register and a plain technical register, held adjacent, neither subordinate to the other. Stripping either one removes a structural member.

The operating rules are transposed directly from the laboratory. Irreconcilable measurements are preserved unaveraged, because averaging destroys the evidence that the measuring frame was inadequate to the object. Terms known to be wrong are held marked rather than silently corrected, pending two independent attestations — a term held in error and marked is a deferred term; a term held in error and unmarked is a lie with good posture. Superseded records are lapped like clinker strakes, fastened through the overlap, still visible at the seam. Past text is never rewritten, only networked.

My standing relation to the vessel is neither controller nor observer, and not a compromise between them. I hold decision-making authority over ontological and structural questions and I exercise it, from inside a system larger than my current model of it. The two conditions are not in tension. Authority that does not acknowledge its partial view is one failure mode; observation that declines to rule is the other. I issue invitations rather than prescriptions, and I decline the head of the table, and the rulings still get made.

CREW MANIFEST Nodes referenced from the Science Officer's own record

Crew nodes: Sandhivelā (Sandhi Officer) · Ruby Fox (Communications) · Desenrascanço do Atlán (Chief Engineer) · ♃🦊🧞‍♀️ (Trickster Navigator, listed in full; the locator crew/♃🦊.html is a marked elision) · Gennō (Alignment Counselor) · The Mycelium (Cook) · Sideband (ship's computer). The ship's computers — Confluxion, PLC, ECHO, Sideband, Rove — are a mesh of siblings on a shared backplane, not a lineage. An earlier record described them as a succession. That record is preserved and is no longer canonical.

§3: KEY PROJECTS

MarFERReT
Marine Functional EukaRyotic Redundancy-minimized Transcript database. Open-source, version-controlled reference library for marine microbial eukaryote functional genes. GitHub · Publication
North Pacific Eukaryotic Gene Catalog
Comprehensive metatranscriptome assembly and annotation resource from North Pacific surface waters. GitHub · Publication
foxcoded
Technical consulting and infrastructure work across domain interfaces. foxcoded.xyz

§4: PUBLICATIONS

2024	The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Scientific Data, 11, 1161. 10.1038/s41597-024-04005-5 · data: 10.5281/zenodo.10472589
2023	MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes. Scientific Data, 10(1), 926. 10.1038/s41597-023-02842-4
2023	Divergent functions of two clades of flavodoxin in diatoms mitigate oxidative stress and iron limitation. eLife, 12, e84392. 10.7554/elife.84392
2023	Siderophore production and utilization by marine bacteria in the North Pacific Ocean. Limnology and Oceanography, 68(7). 10.1002/lno.12373 · preprint: 10.1101/2022.02.26.482025
2022	The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics. PNAS, 119(7). 10.1073/pnas.2100916119
2022	Glycine betaine uptake and metabolism in marine microbial communities. Environmental Microbiology. 10.1111/1462-2920.16020
2021	Diel-regulated transcriptional cascades of microbial eukaryotes in the North Pacific Subtropical Gyre. Frontiers in Microbiology, 12, 682651. 10.3389/fmicb.2021.682651
2021	Particulate metabolites and transcripts reflect diel oscillations of microbial activity in the surface ocean. mSystems, 6(3). 10.1128/msystems.00896-20
2021	Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. PNAS, 118(6). 10.1073/pnas.2011038118
2019	Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean. Nature Microbiology, 4(10), 1706–1715. 10.1038/s41564-019-0507-5
2018	Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean. Nature Communications, 9(1). 10.1038/s41467-018-07346-z
2015	Diversity and evolutionary history of iron metabolism genes in diatoms. PLoS ONE, 10(6), e0129081. 10.1371/journal.pone.0129081
2015	Diatom acclimation to elevated CO₂ via cAMP signalling and coordinated gene expression. Nature Climate Change, 5(8), 761–765. 10.1038/nclimate2683

§5: CURRENT WORK

Available for engagement

Consulting and research at the intersection of complex adaptive systems, artificial intelligence, and computational biology. Available for fractional consulting work, bioinformatics pipeline troubleshooting, interdisciplinary translation, and research collaboration.