  We compute standard model penguin amplitudes in nonleptonic B-decays to light
charmless mesons using tree amplitude data to fix hadronic parameters. The
leading calculation is carried out for the alphas(mb) penguin contributions
from charm quark, up quark, and magnetic penguin loops in the NDR and HV
renormalization schemes. Power suppressed penguins that are proportional to the
chiral condensate are also computed using a new factorization formula for these
terms, which is derived working to all orders in alphas(sqrt{mb\Lambda}). We
demonstrate using SCET1 that this formula exhibits only small perturbative
phases and does not have endpoint singularities. Due to our use of data to fix
hadronic parameters we obtain significantly more accurate predictions for the
short-distance standard model penguin amplitudes than have been found in the
past. Analyzing data in B-> pi pi, B->K pi, and B->rho rho for the penguin
amplitudes we find that standard model short-distance imaginary parts are an
order of magnitude smaller than current measurements, while real parts are up
to a factor of two smaller with the correct sign. This difference is most
likely a consequence of long-distance charm contributions or new physics.
Constraints on the type of new physics that could help explain the data are
derived, and used to show that current data favors sizeable long-distance
strong phases.
