Introducing Seanome
Unlocking Nature's Ancient Wisdom Through Marine Genomics
Hello, World.
I'm Olga Botvinnik, and I'm thrilled to welcome you to Seanome's journey. As the founder of this non-profit focused research organization (FRO), I'm here to share our mission to revolutionize how we understand and learn from ocean biodiversity.
Why the ocean?
The ocean harbors an untapped library of genetic innovation, refined by 4 billions years of evolution. As the primary home to 70% of all animal phyla1, aquatic environments are a living laboratory of innovative body plans, immune systems, and nervous systems far more diverse than on land. Yet today, our understanding of biodiversity remains remarkably narrow — we focus on less than 1% of animal species 2, primarily those directly relevant to drug development. The inequality in our knowledge is staggering: human genetic data is 2,000,000x more enriched in high-quality sequence databases3 — we’re talking Egyptian Pharaoh levels of inequality here — than it would be if our research efforts were distributed equally across species.
Life underwater faces extraordinary evolutionary pressures: marine organisms battle an unprecedented barrage of pathogens, with 70% of marine biomass being microbial4 and a single teaspoon of seawater holds a staggering 100 million viruses5. This has driven the evolution of sophisticated immune systems with potential applications from novel antibiotics to innovative therapies. Marine biology has already revolutionized our field once. Green Fluorescent Protein (GFP), initially isolated from jellyfish in 19626, became biology’s microscopic flashlight in the 1990s7, leading to a Nobel Prize for its discovery. Today, GFP-like fluorescent proteins are are indispensable tools in virtually every cell biology lab worldwide. Like GFP, revolutionary discoveries swim past us every day. A vast molecular library lies beneath the waves — we're building the computational tools to decode its ancient wisdom.
Tools for Biodiversity Breakthroughs
At Seanome, we decode biology's greatest mysteries: genes whose functions remain completely unknown. These "mystery genes" resist classification by commonly used tools like BLAST and HMMer, and even by sophisticated AI approaches such as FoldSeek, returning zero results — no homologs, no structural matches, no interpretable patterns. Where existing methods reach their their detection limits, we're developing sensitive algorithms to reveal hidden molecular functions.
Our mission is to unlock breakthroughs from ocean biodiversity by building open genomics tools
More technically, we build tools to find genes with similar functions but very different sequences (”functional homologs”). For example, the apoptosis regulators BCL2 (human) and ced9 (Caenorhabditis elegans) have only ~20% sequence similarity (much lower than the 50% minimum commonly used for identifying homologous genes!), and yet, they are functionally interchangeable. If BCL2 is deleted in human cells and ced9 is inserted → get the same function, and similarly, if ced9 is deleted in C. elegans, and human BCL2 is inserted→ get the same function8.
Our ultimate goal is ambitious: to decode every protein in the living world. We're starting with the ocean — a deep reservoir of undiscovered molecular innovations. By building open tools to reveal hidden molecular patterns, we're democratizing access to nature's library — accelerating global discovery of nature’s solutions to complex challenges.
Open-sourcing life’s code
At Seanome, we build computational frameworks that amplify scientific discovery. Using Nextflow, Python, and Rust, (and maybe even more languages!) we create open-source tools that empower thousands of scientists worldwide. Each research project we undertake serves dual purposes: advancing specific scientific knowledge while developing tools to empower the broader scientific community to make more discoveries, faster.
Our vision is to open-source the code of life, empowering humanity’s transformation to a world guided by nature's ancient wisdom
We're at a crucial turning point, where biodiversity is becoming not just about conservation, but our first line of defense against challenges ranging from disease, climate, or personal care.
What’s Next: Arctic Clams and Beyond
Our journey begins with an extraordinary discovery driven by personal mission. When Max Glanz, our collaborator at University of Florida, set out to find a cure for his father's rare neurodegenerative disease, he made a remarkable finding: Arctic clams naturally tolerate lipids toxic to human neurons. Next week, we'll dive into the science behind this remarkable adaptation.
Thanks to Claude for editing.
Footnotes
The “2,000,000x enriched” number comes from here: As of Nov 14th, 2024, UniProtKB Reviewed (Swiss-Prot) contains 109,973 entries for animals [metazoans, (taxonomy_id:33208)], and 20,428 of those are human. 20,428/109,973 = 0.18575…, which we can round to 0.2. Then, we assume equal distribution and similar numbers of genes for all 10,000,000 predicted animal species (see reference 3 below), which maybe an overestimate, but a useful order of magnitude. If human is 1/10,000,000 animals species, then we calculate enrichment as 0.2/(1/10,000,000) = 2,000,000.
UniProt KB Search Screenshot:
The “less than 1% of animal species” number comes from the four main species used for drug discovery are human, mouse, rat, and monkeys, compared to the 10,000,000 predicted animal species predicted by Mora, C., Tittensor, D. P., Adl, S., Simpson, A. G. B. & Worm, B. How Many Species Are There on Earth and in the Ocean? PLoS Biol. 9, e1001127-8 (2011). The 10 million number is a conservative estimate, as we probably are severly undercounting arthropod (e.g. insects, spiders, mites, ticks) species, as discussed in Wiens, J. J. How many species are there on Earth? Progress and problems. PLoS Biol. 21, e3002388 (2023).
This is awesome to see! I'm always a fan of FROs doing speculative research in underexplored areas, and there aren't many places less-explored than the ocean. I'm convinced that pretty much every biological function you'd ever want exists out in nature somewhere, so I can't wait to see what you find!