how do you shift the bottoms of bars in pgfplots?

If I understand you correctly, you can use the log origin option, as suggested by this answer over on TeX.SE:

\documentclass{standalone}
\usepackage{pgfplots}
\begin{document}
\begin{tikzpicture}
  \begin{semilogyaxis}[log origin=infty]
    \addplot+[ybar] coordinates {(0, 10) (1, 0.01)};
  \end{semilogyaxis}
\end{tikzpicture}
\end{document}