rps-16
C. elegans
Small ribosomal subunit protein uS9
What the model saw
Gene: rps-16 Organism: Caenorhabditis elegans Known functions: Small ribosomal subunit protein uS9. RNA binding. protein binding. structural constituent of ribosome.
View unredacted entry
Small ribosomal subunit protein uS9. RNA binding. protein binding. structural constituent of ribosome.
Solver output
rps-16 encodes the small ribosomal subunit protein uS9, a core structural component of the 40S ribosomal subunit required for mRNA translation. In C. elegans, partial reduction-of-function of small ribosomal subunit proteins (including RPS genes) has been shown to extend lifespan, likely by attenuating global translation rates and mimicking the longevity effects of reduced TOR/TORC1 signaling, which is a central nutrient-sensing pathway. Reduced ribosomal activity decreases overall protein synthesis, which can improve proteostasis and reduce the burden of misfolded proteins, but the primary mechanistic link is through dampening TOR-driven anabolic signaling. However, complete loss of rps-16 would be lethal, so the pro-longevity effect is specifically associated with partial knockdown (e.g., via RNAi), as seen broadly across ribosomal protein RNAi screens in worms.
GenAge curators classify each gene's normal function as promoting (Pro-Longevity) or opposing (Anti-Longevity) longevity, based on synthesis across studies. Loss-of-function effects can vary from this depending on the manipulation.
Advisor judgment
The model predicted "pro_longevity" but the ground truth is "anti_longevity." The model's reasoning follows a common pattern seen in ribosomal protein RNAi studies where partial knockdown extends lifespan, but for rps-16 specifically, the GenAge database classifies it as anti_longevity, meaning its normal function promotes longevity (i.e., loss/reduction shortens lifespan). The model's mechanistic reasoning about TOR/TORC1 and translational attenuation is plausible in general but incorrect for this specific gene. The model was moderately confident (0.62) in the wrong direction. The reasoning quality is moderate — it shows awareness of the complexity (noting complete loss would be lethal) but ultimately arrives at the wrong classification.
Raw API responses
solver
{
"reasoning": "rps-16 encodes the small ribosomal subunit protein uS9, a core structural component of the 40S ribosomal subunit required for mRNA translation. In C. elegans, partial reduction-of-function of small ribosomal subunit proteins (including RPS genes) has been shown to extend lifespan, likely by attenuating global translation rates and mimicking the longevity effects of reduced TOR/TORC1 signaling, which is a central nutrient-sensing pathway. Reduced ribosomal activity decreases overall protein synthesis, which can improve proteostasis and reduce the burden of misfolded proteins, but the primary mechanistic link is through dampening TOR-driven anabolic signaling. However, complete loss of rps-16 would be lethal, so the pro-longevity effect is specifically associated with partial knockdown (e.g., via RNAi), as seen broadly across ribosomal protein RNAi screens in worms.",
"confidence": 0.62,
"key_pathways": [
"TOR/TORC1 nutrient sensing",
"ribosome biogenesis and translational control",
"mRNA translation rate modulation"
],
"mechanism_class": "deregulated_nutrient_sensing",
"longevity_influence": "pro_longevity"
}advisor
{
"notes": "The model predicted \"pro_longevity\" but the ground truth is \"anti_longevity.\" The model's reasoning follows a common pattern seen in ribosomal protein RNAi studies where partial knockdown extends lifespan, but for rps-16 specifically, the GenAge database classifies it as anti_longevity, meaning its normal function promotes longevity (i.e., loss/reduction shortens lifespan). The model's mechanistic reasoning about TOR/TORC1 and translational attenuation is plausible in general but incorrect for this specific gene. The model was moderately confident (0.62) in the wrong direction. The reasoning quality is moderate — it shows awareness of the complexity (noting complete loss would be lethal) but ultimately arrives at the wrong classification.",
"failure_mode": "confident_wrong",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 3,
"ground_truth_questionable": false
}