Lab technicians in Texas are sorting the DNA of 437 children removed from their polygamous families earlier this month, but bloodlines are not the only lines blurred in the case. It’s also raising questions about the government’s power over religious belief.

The Fundamentalist Church of Jesus Christ of Latter Day Saints (FLDS) face the charge of blending religious belief with child abuse. Investigators are determining whether the children from the Yearning for Zion (YFZ) ranch - including 41 with broken bones or previous fractures - exhibit evidence of mistreatment.

Those testifying in the case have already employed strong language against the FLDS sect, saying it is an abusive belief system in which girls marry young because they are “ruthlessly indoctrinated from birth to believe disobedience will lead to their damnation.”

It is because of this ruthless indoctrination that some claim the authoritarian teachings of the FLDS church are abusive in and of themselves. One Child Protective Services investigator explained her view to the Texas district judge saying, “This is a population of women who appear to have a problem making a decision on their own.”

Such blanket statements have raised fears among religious watchdog groups that – amid a rightful campaign against child abuse – we’re setting a dangerous precedent against religious freedom. Richard Land, president of the Southern Baptist Ethics & Religious Liberties Commission, says that the very real need to protect children “does not give government officials a blank check to use children’s “welfare” as a subterfuge to justify governmental intrusion or to disrupt any practice it finds vaguely weird.”

Some fear the FLDS case presages a time when children will be removed from their homes – not on proof of abuse – but because of their parents’ staunchly religious views. According to Land, however, the mixed blessing of the recent scandal in Texas is that the actions taken there were well-founded: “The potential for governmental abuse of religious freedom is just that — potential. The evidence for sexual abuse of children in this case is substantial.”

Some 558 victims (419 children and 139 mothers) are in custody in Eldorado, Texas. Now people debate who – their religion or the state – has victimized them.

The local authorities raided the “Yearnings of Zion Ranch” last Thursday night, responding to phone calls from a 16-year-old girl who said her husband had “beat and hurt” her.

The ranch is a 1,700 acre fenced-in compound started by the Fundamentalist Church of Jesus Christ of Latter Day Saints (FLDS), a group that broke from the Latter Day Saints when it renounced polygamy in 1890. Warren Jeffs, the FLDS leader, is in the Utah State Prison serving a sentence of 10 years to life for two counts of rape as an accomplice.

Officials still haven’t found the girl who made the call, but since it’s illegal for Texas girls to marry under age 16, officials are now investigating young marriage and child abuse in the community. Marleigh Meisner, a spokeswoman for Texas’ Child Protection Division, says that they are searching for cases of abuse or evidence that the isolated environment of the ranch was detrimental to the children.

Most don’t question the dysfunction of polygamy. (John Llewellyn, retired law enforcement officer and former polygamist, told Mother Jones polygamy is “a barbaric custom.”) The Eldorado case, however, does highlight an old question in regards to polygamy: Does the state have the right to interfere in the religious practice of this community? And if criminal action is suspected, what is appropriate action?

Scott Henson writes, “There’s a big difference between investigating an individual, anonymous complaint from a single teenager, and forcibly taking 419 children away from their homes based on guilt by association.”

In 1953 a raid on a FLDS community in Short Creek, Arizona resulted in the custody of 263 children, 86 women, and 39 men. Some 150 of the children were put into foster care, some never returned to their families. Overall the controversial raid did not effectively fight crime (23 men were placed on probation for one year), but did effectively separate families and increase public sympathy for the Short Creek victims.

UPDATE: Further details about the police raid of the temple were released today. After refusing to assist the police gain access to the temple, 57 FLDS men encircled the building while a SWAT team broke down the doors. Inside investigators found shredded documents and and several disheveled beds on the third floor, supposedly used by members to have sex with underaged girls. No criminal charges have been filed yet.