Gee believes that all fossils are 'transitional' because:
"if we didn't have ancestors, then we wouldn't be here."
It's his faith in evolution he is referring to, not scientific proof for it.
"That it is impossible to trace direct lineages of ancestry and descent from the fossil record should be self-evident. Ancestors must exist, of course -- but we can never attribute ancestry to any particular fossil we might find. Just try this thought experiment -- let's say you find a fossil of a hominid, an ancient member of the human family. You can recognize various attributes that suggest kinship to humanity, but you would never know whether this particular fossil represented your lineal ancestor - even if that were actually the case. The reason is that fossils are never buried with their birth certificates. Again, this is a logical constraint that must apply even if evolution were true -- which is not in doubt, because if we didn't have ancestors, then we wouldn't be here. Neither does this mean that fossils exhibiting transitional structures do not exist, nor that it is impossible to reconstruct what happened in evolution. Unfortunately, many paleontologists believe that ancestor/descendent lineages can be traced from the fossil record, and my book is intended to debunk this view. However, this disagreement is hardly evidence of some great scientific coverup -- religious fundamentalists such as the DI -- who live by dictatorial fiat -- fail to understand that scientific disagreement is a mark of health rather than decay. However, the point of IN SEARCH OF DEEP TIME, ironically, is that old-style, traditional evolutionary biology -- the type that feels it must tell a story, and is therefore more appealing to news reporters and makers of documentaries -- is unscientific."
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Let's break it down for you.
He is a scientist who accepts the validity of the theory of evolution and common descent.
His quotation had nothing to do with any dispute about the validity of Lucy as a transitional. Beyond that, his point in "In Search of Deep Time" was only that researchers should not claim direct lineage that they can't establish with evidence. No one here in this thread claimed that Lucy was ancetoral to humans. She was, however, transitional and neither Gee nor competent scientists deny that fact.
He was specifically talking about how creationists misrepresent his views to support a position that neither he nor the evidence supports.
Finally, I think he sums up your problem pretty nicely in point 4 of his response to Jonathan Wells dishonest quote mining.
"In addition, the use by creationists of selective, unauthorized quotations, possibly with intent to mislead the public undermines their position as self-appointed guardians of public values and morals."