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So we are left with the eminal question: What's wrong with the standard solar model?
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What's an eminal question?
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Isn't it fairly obvious what's up? There is a discrepancy between the interpretive implications of the helioseismic observations, and the interpretive implications of the spectral data. Both are complicated affairs, and the discrepency remains to be explained.
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Ok, so doesn't a discrepancy show that something is wrong with the standard solar model?
The authors of all three papers think it is a big deal , maybe you don't so could you explain why the Neon discrepancy is no big deal, maybe some links?
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Since around 0.995 solar radii, the variation switches from in-phase to anti-phase, it could suggest a "skin deep" effect, but not necessarily that the magnetic field is actually generated so close to the surface. It could also suggest that the field, generated near the tachocline, is subject to turbulent shear, and reconfigures itself (a poloidal -> toroidal transition, perhaps?) near the surface. That would be consistent with the generation of sunspots due to shearing of the field.
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So what is the evidence that a deep layer is responsible for the magnetic fields? It seems to me that the skin deep explanation works for the entire solar surface, not just for sunspots. If you say "but not necessarily that the magnetic field is actually generated so close to the surface" what is the evidence against such a claim?
Cheers.