{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:2JMUUOV5EYKKHVKKOUG44LA2NJ","short_pith_number":"pith:2JMUUOV5","canonical_record":{"source":{"id":"2407.15908","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.OT","submitted_at":"2024-07-22T16:41:25Z","cross_cats_sorted":[],"title_canon_sha256":"c76ce5e075c83d355507771a7e25a05c5566819f7c829e18a487d51c75d11ef5","abstract_canon_sha256":"6ba9f2f442fca9f378b9a8280cc9ee4e525815d29beea4f605f762fd426d9e31"},"schema_version":"1.0"},"canonical_sha256":"d2594a3abd2614a3d54a750dce2c1a6a5027a8533b532926d03332a361636a3f","source":{"kind":"arxiv","id":"2407.15908","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2407.15908","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"arxiv_version","alias_value":"2407.15908v2","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2407.15908","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"pith_short_12","alias_value":"2JMUUOV5EYKK","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"pith_short_16","alias_value":"2JMUUOV5EYKKHVKK","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"pith_short_8","alias_value":"2JMUUOV5","created_at":"2026-07-05T10:01:34Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:2JMUUOV5EYKKHVKKOUG44LA2NJ","target":"record","payload":{"canonical_record":{"source":{"id":"2407.15908","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.OT","submitted_at":"2024-07-22T16:41:25Z","cross_cats_sorted":[],"title_canon_sha256":"c76ce5e075c83d355507771a7e25a05c5566819f7c829e18a487d51c75d11ef5","abstract_canon_sha256":"6ba9f2f442fca9f378b9a8280cc9ee4e525815d29beea4f605f762fd426d9e31"},"schema_version":"1.0"},"canonical_sha256":"d2594a3abd2614a3d54a750dce2c1a6a5027a8533b532926d03332a361636a3f","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:01:34.759078Z","signature_b64":"6wR7RXE0RVX7gOFhLYeWCa+9d3hDLYNl3HjsGkTwGeLI1Qwhd2+j8nHYWOnObVDDp6xFZXtWAyzkWd2bmzTjBA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"d2594a3abd2614a3d54a750dce2c1a6a5027a8533b532926d03332a361636a3f","last_reissued_at":"2026-07-05T10:01:34.758603Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:01:34.758603Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2407.15908","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T10:01:34Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"GK6I3sFYDRjTQXsZl91Vftm+uhfoy7neBra8nBzJ0bGxrcQbWT0C3YY5fUdaaief+MTA4WoI8gMwnARjJ1K6BQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-13T13:48:32.920336Z"},"content_sha256":"52948942652b6ab0d01342329d882da14c2a4e64cc64a837585a406017311bde","schema_version":"1.0","event_id":"sha256:52948942652b6ab0d01342329d882da14c2a4e64cc64a837585a406017311bde"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:2JMUUOV5EYKKHVKKOUG44LA2NJ","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"The Genomic Code: The genome instantiates a generative model of the organism","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.OT","authors_text":"Kevin J. Mitchell, Nick Cheney","submitted_at":"2024-07-22T16:41:25Z","abstract_excerpt":"How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this scheme, by analogy with variational autoencoders, the genome comprises a connectionist network, embodying a compressed space of latent variables, with weights that get encoded by the learning algorithm of evolution and decoded through the processes of development. The generative model analogy accounts for the complex, distributed genetic architecture of most trai"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2407.15908","kind":"arxiv","version":2},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2407.15908/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T10:01:34Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"MKv0WNfhPlFKp1E4oXBbiVob3ESgF5AUpjdEdXagBi/r2WOrEyhx5Zc14crjRwytro5FDJCFzJZQIEgrfRiPAw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-13T13:48:32.920869Z"},"content_sha256":"55b72d98f25be0b6389a63149c821ac0896bb4eb052ed573bab4ff9f784e5043","schema_version":"1.0","event_id":"sha256:55b72d98f25be0b6389a63149c821ac0896bb4eb052ed573bab4ff9f784e5043"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/2JMUUOV5EYKKHVKKOUG44LA2NJ/bundle.json","state_url":"https://pith.science/pith/2JMUUOV5EYKKHVKKOUG44LA2NJ/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/2JMUUOV5EYKKHVKKOUG44LA2NJ/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-08-13T13:48:32Z","links":{"resolver":"https://pith.science/pith/2JMUUOV5EYKKHVKKOUG44LA2NJ","bundle":"https://pith.science/pith/2JMUUOV5EYKKHVKKOUG44LA2NJ/bundle.json","state":"https://pith.science/pith/2JMUUOV5EYKKHVKKOUG44LA2NJ/state.json","well_known_bundle":"https://pith.science/.well-known/pith/2JMUUOV5EYKKHVKKOUG44LA2NJ/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:2JMUUOV5EYKKHVKKOUG44LA2NJ","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"6ba9f2f442fca9f378b9a8280cc9ee4e525815d29beea4f605f762fd426d9e31","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.OT","submitted_at":"2024-07-22T16:41:25Z","title_canon_sha256":"c76ce5e075c83d355507771a7e25a05c5566819f7c829e18a487d51c75d11ef5"},"schema_version":"1.0","source":{"id":"2407.15908","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2407.15908","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"arxiv_version","alias_value":"2407.15908v2","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2407.15908","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"pith_short_12","alias_value":"2JMUUOV5EYKK","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"pith_short_16","alias_value":"2JMUUOV5EYKKHVKK","created_at":"2026-07-05T10:01:34Z"},{"alias_kind":"pith_short_8","alias_value":"2JMUUOV5","created_at":"2026-07-05T10:01:34Z"}],"graph_snapshots":[{"event_id":"sha256:55b72d98f25be0b6389a63149c821ac0896bb4eb052ed573bab4ff9f784e5043","target":"graph","created_at":"2026-07-05T10:01:34Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2407.15908/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this scheme, by analogy with variational autoencoders, the genome comprises a connectionist network, embodying a compressed space of latent variables, with weights that get encoded by the learning algorithm of evolution and decoded through the processes of development. The generative model analogy accounts for the complex, distributed genetic architecture of most trai","authors_text":"Kevin J. Mitchell, Nick Cheney","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.OT","submitted_at":"2024-07-22T16:41:25Z","title":"The Genomic Code: The genome instantiates a generative model of the organism"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2407.15908","kind":"arxiv","version":2},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:52948942652b6ab0d01342329d882da14c2a4e64cc64a837585a406017311bde","target":"record","created_at":"2026-07-05T10:01:34Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"6ba9f2f442fca9f378b9a8280cc9ee4e525815d29beea4f605f762fd426d9e31","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.OT","submitted_at":"2024-07-22T16:41:25Z","title_canon_sha256":"c76ce5e075c83d355507771a7e25a05c5566819f7c829e18a487d51c75d11ef5"},"schema_version":"1.0","source":{"id":"2407.15908","kind":"arxiv","version":2}},"canonical_sha256":"d2594a3abd2614a3d54a750dce2c1a6a5027a8533b532926d03332a361636a3f","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"d2594a3abd2614a3d54a750dce2c1a6a5027a8533b532926d03332a361636a3f","first_computed_at":"2026-07-05T10:01:34.758603Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:01:34.758603Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"6wR7RXE0RVX7gOFhLYeWCa+9d3hDLYNl3HjsGkTwGeLI1Qwhd2+j8nHYWOnObVDDp6xFZXtWAyzkWd2bmzTjBA==","signature_status":"signed_v1","signed_at":"2026-07-05T10:01:34.759078Z","signed_message":"canonical_sha256_bytes"},"source_id":"2407.15908","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:52948942652b6ab0d01342329d882da14c2a4e64cc64a837585a406017311bde","sha256:55b72d98f25be0b6389a63149c821ac0896bb4eb052ed573bab4ff9f784e5043"],"state_sha256":"f042d88a049acd1c4fe7ade540673689a8c578171c3a0f9644a314be0a33603e"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"XbuW5AQ8mrKfVMyydBMjDzH279hoWh1sr3BkKW+W3vudv5y9Q5J8wG/DtR1oYhZ426TiOqzOGmIHGeaOWbWzBQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-13T13:48:32.965598Z","bundle_sha256":"0e20001bcae69b1719ff17be8c662aa32f716b2d3fee20b9c96cf8ab4f07f938"}}