Of the text --The USPTO issued rejections based not only on prior art documents filed with the petition for reexamination, but also based on additional references newly found by the USPTO which brought into question the novelty and non-obviousness of Thomson’s original patent claims. To support their petition, the petitioners for reexamination of the patents cited several prior art documents, including papers published between 1982 and 1990 that detail a process for deriving embryonic stem cells from mammals. In addition, Dr. Jeanne Loring of the Burnham Institute, a well respected and world renowned stem cell research scientist, submitted supporting evidence to the USPTO. --, a discussion of the rejection in re-examination of the claims of US 5,843,780 appears at
http://ipbiz.blogspot.com/2007/04/first-office-action-rejects-claims-of.html

Of -- on additional references newly found by the USPTO which brought into question the novelty and non-obviousness of Thomson’s original patent claims. --, the NEWLY APPLIED reference in the re-exam of the '780 was a paper by Bongso which

#1. was cited in the '780 patent [Bongso, et al., "Isolation and culture of inner cell mass cells from human blastocysts", Human Reproduction, 9:2110-2117, 1994. ]
#2. was mis-cited in the re-exam [9 Human Reproduction 2110 (1984), not exactly showing great care in proofreading NOW or analysis at the time of the application.]

Of --from mammals--, the key text at issue with the Williams patent is --from animals including, but not limited to, humans and a number of other animal species such as birds (e.g. chickens), mice, sheep, pigs, cattle, goats and fish.-- There is going to be a major league enablement issue of Williams as to "humans."

Separately, the declaration of Loring played no part in the rejections.

Although it is certainly correct to say the issue is the novelty and nonobviousness of the claims of Thomson / WARF, one notes that a manner to establish this will be evaluating the enablement of the cited prior art.