149 lines
19 KiB
Text
149 lines
19 KiB
Text
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Researching: How many amino acids are encoded by the standard genetic code?
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{"question": "How many amino acids are encoded by the standard genetic code?", "depth": "balanced", "max_iterations": 5, "token_budget": 20000, "model_id": "claude-sonnet-4-6", "event": "research_started", "trace_id": "7561029e-5dcb-4eaa-98e9-7496ed4bf4c2", "researcher": "web", "logger": "marchwarden.researcher.web", "level": "info", "timestamp": "2026-04-09T01:52:58.449581Z"}
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{"step": 1, "decision": "Beginning research: depth=balanced", "question": "How many amino acids are encoded by the standard genetic code?", "context": "", "max_iterations": 5, "token_budget": 20000, "event": "start", "trace_id": "7561029e-5dcb-4eaa-98e9-7496ed4bf4c2", "researcher": "web", "logger": "marchwarden.researcher.trace", "level": "info", "timestamp": "2026-04-09T01:52:58.449885Z"}
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{"step": 28, "decision": "Research complete", "confidence": 0.98, "citation_count": 4, "gap_count": 1, "discovery_count": 2, "total_duration_sec": 65.235, "event": "complete", "trace_id": "7561029e-5dcb-4eaa-98e9-7496ed4bf4c2", "researcher": "web", "logger": "marchwarden.researcher.trace", "level": "info", "timestamp": "2026-04-09T01:54:01.507373Z"}
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{"trace_id": "7561029e-5dcb-4eaa-98e9-7496ed4bf4c2", "confidence": 0.98, "citations": 4, "tokens_used": 48308, "wall_time_sec": 63.05677556991577, "event": "ask_completed", "logger": "marchwarden.cli", "level": "info", "timestamp": "2026-04-09T01:54:01.785150Z"}
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╭─────────────────────────────────── Answer ───────────────────────────────────╮
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│ The standard genetic code encodes 20 common amino acids. These are specified │
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│ by 64 possible codons (combinations of three nucleotides from four bases), │
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│ with most amino acids encoded by more than one codon (a property called │
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│ degeneracy). Methionine and tryptophan are the only amino acids specified by │
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│ a single codon each. Three codons serve as stop signals rather than encoding │
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│ amino acids. Beyond the standard 20, two additional amino │
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│ acids—selenocysteine (the 21st) and pyrrolysine (the 22nd)—are also │
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│ genetically encoded in certain organisms via reprogramming of stop codons │
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│ UGA and UAG, respectively, but are not part of the standard set of 20. │
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╰──────────────────────────────────────────────────────────────────────────────╯
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Citations
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┏━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┓
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┃ # ┃ Title / Locator ┃ Excerpt ┃ Conf ┃
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┡━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━┩
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│ 1 │ The genetic code (article) - │ Most of the amino acids in the │ 0.95 │
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│ │ Khan Academy │ genetic code are encoded by at │ │
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│ │ https://www.khanacademy.org/s │ least two codons. In fact, │ │
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│ │ cience/hs-bio/x230b3ff252126b │ methionine and tryptophan are │ │
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│ │ b6:gene-expression-and-regula │ the only amino acids specified │ │
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│ │ tion/x230b3ff252126bb6:untitl │ by a single codon. │ │
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│ │ ed-348/a/the-genetic-code │ │ │
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├─────┼───────────────────────────────┼────────────────────────────────┼───────┤
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│ 2 │ Is there a twenty third amino │ The universal genetic code │ 0.98 │
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│ │ acid in the genetic code? - │ includes 20 common amino │ │
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│ │ PubMed │ acids. In addition, │ │
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│ │ https://pubmed.ncbi.nlm.nih.g │ selenocysteine (Sec) and │ │
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│ │ ov/16713651/ │ pyrrolysine (Pyl), known as │ │
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│ │ │ the twenty first and twenty │ │
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│ │ │ second amino acids, are │ │
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│ │ │ encoded by UGA and UAG, │ │
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│ │ │ respectively, which are the │ │
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│ │ │ codons that usually function │ │
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│ │ │ as stop signals. │ │
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├─────┼───────────────────────────────┼────────────────────────────────┼───────┤
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│ 3 │ Genetic code - Wikipedia │ The genetic code is highly │ 0.95 │
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│ │ https://en.wikipedia.org/wiki │ similar among all organisms │ │
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│ │ /Genetic_code │ and can be expressed in a │ │
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│ │ │ simple table with 64 entries. │ │
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│ │ │ The codons specify which amino │ │
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│ │ │ acid will be added next during │ │
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│ │ │ protein biosynthesis. │ │
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├─────┼───────────────────────────────┼────────────────────────────────┼───────┤
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│ 4 │ Understanding the Genetic │ The universal │ 0.97 │
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│ │ Code - PMC │ triple-nucleotide genetic │ │
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│ │ https://pmc.ncbi.nlm.nih.gov/ │ code, allowing DNA-encoded │ │
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│ │ articles/PMC6620406/ │ mRNA to be translated into the │ │
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│ │ │ amino acid sequences of │ │
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│ │ │ proteins using transfer RNAs │ │
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│ │ │ (tRNAs) and many accessory and │ │
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│ │ │ modification factors, is │ │
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│ │ │ essentially common to all │ │
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│ │ │ living organisms on Earth. │ │
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└─────┴───────────────────────────────┴────────────────────────────────┴───────┘
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Gaps
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┏━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
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┃ Category ┃ Topic ┃ Detail ┃
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┡━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
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│ scope_exceeded │ Exact codon-to-amino-acid │ The full detailed codon │
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│ │ mapping table │ table listing all 64 codons │
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│ │ │ and their corresponding │
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│ │ │ amino acids was not │
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│ │ │ extracted verbatim from the │
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│ │ │ sources, though the total │
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│ │ │ count of 20 standard amino │
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│ │ │ acids is well established. │
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└────────────────┴──────────────────────────────┴──────────────────────────────┘
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Discovery Events
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┏━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┓
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┃ ┃ Suggested ┃ ┃ ┃
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┃ Type ┃ Researcher ┃ Query ┃ Reason ┃
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┡━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━┩
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│ related_research │ database │ selenocysteine │ The PubMed source │
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│ │ │ pyrrolysine │ raises the │
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│ │ │ genetic code │ question of │
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│ │ │ expansion │ expanded genetic │
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│ │ │ organisms │ codes beyond 20 │
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│ │ │ │ amino acids, │
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│ │ │ │ which may be │
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│ │ │ │ relevant for │
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│ │ │ │ advanced biology │
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│ │ │ │ research. │
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├──────────────────┼───────────────────┼───────────────────┼───────────────────┤
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│ related_research │ arxiv │ synthetic biology │ Wikipedia │
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│ │ │ unnatural amino │ mentions expanded │
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│ │ │ acids expanded │ genetic codes in │
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│ │ │ genetic code │ synthetic │
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│ │ │ │ biology, │
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│ │ │ │ suggesting active │
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│ │ │ │ research into │
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│ │ │ │ adding more than │
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│ │ │ │ 22 amino acids. │
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└──────────────────┴───────────────────┴───────────────────┴───────────────────┘
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Open Questions
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┏━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
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┃ Priority ┃ Question ┃ Context ┃
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┡━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
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│ medium │ Could a 23rd amino acid ever │ A PubMed study scanned 16 │
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│ │ become widely distributed and │ archaeal and 130 bacterial │
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│ │ genetically encoded in nature? │ genomes for tRNAs corresponding │
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│ │ │ to the three stop codons and │
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│ │ │ concluded that additional │
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│ │ │ widely distributed genetically │
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│ │ │ encoded amino acids are │
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│ │ │ unlikely. │
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├──────────┼─────────────────────────────────┼─────────────────────────────────┤
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│ low │ How many non-standard amino │ Wikipedia references expanded │
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│ │ acids have been successfully │ genetic codes in synthetic │
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│ │ incorporated into proteins via │ biology as a distinct topic, │
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│ │ synthetic biology methods? │ suggesting │
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│ │ │ laboratory-engineered codes may │
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│ │ │ go beyond the natural 22. │
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└──────────┴─────────────────────────────────┴─────────────────────────────────┘
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╭───────────────────────────────── Confidence ─────────────────────────────────╮
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│ Overall: 0.98 │
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│ Corroborating sources: 4 │
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│ Source authority: high │
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│ Contradiction detected: False │
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│ Query specificity match: 1.00 │
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│ Budget status: under cap │
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│ Recency: current │
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╰──────────────────────────────────────────────────────────────────────────────╯
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╭──────────────────────────────────── Cost ────────────────────────────────────╮
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│ Tokens: 48308 │
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│ Iterations: 4 │
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│ Wall time: 63.06s │
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│ Model: claude-sonnet-4-6 │
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╰──────────────────────────────────────────────────────────────────────────────╯
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trace_id: 7561029e-5dcb-4eaa-98e9-7496ed4bf4c2
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