cyc-2.1
C. elegans
Cytochrome c 2.1
What the model saw
Gene: cyc-2.1 Organism: Caenorhabditis elegans Known functions: Cytochrome c 2.1. electron transfer activity. heme binding.
View unredacted entry
Cytochrome c 2.1. electron transfer activity. heme binding.
Solver output
cyc-2.1 encodes a cytochrome c protein in C. elegans, functioning in mitochondrial electron transfer via heme binding. Cytochrome c is a core component of the mitochondrial electron transport chain (ETC), shuttling electrons between Complex III (cytochrome bc1) and Complex IV (cytochrome c oxidase). While robust mitochondrial function is generally associated with health, paradoxically in C. elegans, partial reduction of ETC activity (e.g., via clk-1, isp-1, or nuo-6 mutations) extends lifespan through mitochondrial hormesis and reduced ROS production. Full loss of cytochrome c function would be lethal, but partial reduction could be pro-longevity. Additionally, cytochrome c release into the cytoplasm triggers apoptosis, which can have complex effects on organismal aging. The dual role of cytochrome c in both energy production and apoptosis initiation makes the net longevity influence genuinely ambiguous without loss-of-function data.
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 "unclear" while the ground truth is "anti_longevity." The model's reasoning is thoughtful and covers relevant biology (ETC, mitochondrial hormesis, apoptosis), but it failed to commit to the correct answer. The model correctly identified the mitochondrial ETC role and even noted that partial ETC reduction can extend lifespan in C. elegans, but then hedged too much rather than predicting anti_longevity. Since cyc-2.1 is anti_longevity, this likely means its loss-of-function extends lifespan (consistent with the mitochondrial hormesis argument the model itself raised), but the model didn't commit to this direction. The mechanism discussion was partially relevant but the model didn't correctly resolve the ambiguity it identified. The confidence of 0.45 reflects appropriate uncertainty but the final call of "unclear" is wrong.
Raw API responses
solver
{
"reasoning": "cyc-2.1 encodes a cytochrome c protein in C. elegans, functioning in mitochondrial electron transfer via heme binding. Cytochrome c is a core component of the mitochondrial electron transport chain (ETC), shuttling electrons between Complex III (cytochrome bc1) and Complex IV (cytochrome c oxidase). While robust mitochondrial function is generally associated with health, paradoxically in C. elegans, partial reduction of ETC activity (e.g., via clk-1, isp-1, or nuo-6 mutations) extends lifespan through mitochondrial hormesis and reduced ROS production. Full loss of cytochrome c function would be lethal, but partial reduction could be pro-longevity. Additionally, cytochrome c release into the cytoplasm triggers apoptosis, which can have complex effects on organismal aging. The dual role of cytochrome c in both energy production and apoptosis initiation makes the net longevity influence genuinely ambiguous without loss-of-function data.",
"confidence": 0.45,
"key_pathways": [
"mitochondrial electron transport chain (Complex III-IV electron shuttling)",
"mitochondrial hormesis / retrograde signaling",
"cytochrome c-mediated apoptosis"
],
"mechanism_class": "mitochondrial_dysfunction",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"anti_longevity.\" The model's reasoning is thoughtful and covers relevant biology (ETC, mitochondrial hormesis, apoptosis), but it failed to commit to the correct answer. The model correctly identified the mitochondrial ETC role and even noted that partial ETC reduction can extend lifespan in C. elegans, but then hedged too much rather than predicting anti_longevity. Since cyc-2.1 is anti_longevity, this likely means its loss-of-function extends lifespan (consistent with the mitochondrial hormesis argument the model itself raised), but the model didn't commit to this direction. The mechanism discussion was partially relevant but the model didn't correctly resolve the ambiguity it identified. The confidence of 0.45 reflects appropriate uncertainty but the final call of \"unclear\" is wrong.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 3,
"ground_truth_questionable": false
}