ifd-1
C. elegans
Intermediate filament protein ifd-1
What the model saw
Gene: ifd-1 Organism: Caenorhabditis elegans Known functions: Intermediate filament protein ifd-1. structural constituent of cytoskeleton.
View unredacted entry
Intermediate filament protein ifd-1. structural constituent of cytoskeleton.
Solver output
ifd-1 encodes an intermediate filament protein in C. elegans whose primary annotated function is as a structural constituent of the cytoskeleton. Intermediate filaments provide mechanical integrity to cells, but this structural role alone does not map cleanly onto a canonical pro- or anti-longevity pathway. While cytoskeletal integrity can influence proteostasis and cellular stress responses, the specific contribution of ifd-1 to longevity-relevant signaling (e.g., DAF-16/FOXO, mTOR, or mitochondrial pathways) is not evident from its molecular function annotation alone. Without evidence linking this particular intermediate filament to a defined aging hallmark mechanism, a confident directional prediction cannot be made.
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" with low confidence (0.35), while the ground truth is "anti_longevity." The model's reasoning is plausible given the limited information provided (only structural cytoskeletal function annotation), but it failed to make the correct directional call. The model correctly identified that intermediate filaments relate to cytoskeletal integrity but couldn't connect this to an anti-longevity role. In C. elegans, ifd-1 (intermediate filament D) has been shown to have anti-longevity effects, likely through its role in intestinal integrity and stress responses. The model's uncertainty was somewhat appropriate given the sparse annotation, but the ground truth is clear. This is a case of appropriate uncertainty rather than a confident wrong answer.
Raw API responses
solver
{
"reasoning": "ifd-1 encodes an intermediate filament protein in C. elegans whose primary annotated function is as a structural constituent of the cytoskeleton. Intermediate filaments provide mechanical integrity to cells, but this structural role alone does not map cleanly onto a canonical pro- or anti-longevity pathway. While cytoskeletal integrity can influence proteostasis and cellular stress responses, the specific contribution of ifd-1 to longevity-relevant signaling (e.g., DAF-16/FOXO, mTOR, or mitochondrial pathways) is not evident from its molecular function annotation alone. Without evidence linking this particular intermediate filament to a defined aging hallmark mechanism, a confident directional prediction cannot be made.",
"confidence": 0.35,
"key_pathways": [
"intermediate filament cytoskeletal network",
"mechanical stress response",
"cellular structural integrity"
],
"mechanism_class": "other",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" with low confidence (0.35), while the ground truth is \"anti_longevity.\" The model's reasoning is plausible given the limited information provided (only structural cytoskeletal function annotation), but it failed to make the correct directional call. The model correctly identified that intermediate filaments relate to cytoskeletal integrity but couldn't connect this to an anti-longevity role. In C. elegans, ifd-1 (intermediate filament D) has been shown to have anti-longevity effects, likely through its role in intestinal integrity and stress responses. The model's uncertainty was somewhat appropriate given the sparse annotation, but the ground truth is clear. This is a case of appropriate uncertainty rather than a confident wrong answer.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}