For Gordon Brown - to whom the Bill means so much - and Geoff Hoon, his chief whip, the prospect of a parliamentary defeat on its measures is unthinkable.
Yet that is the uncomfortable position in which they find themselves as a result of the implacable opposition of the Roman Catholic lobby; and it is why, eventually, the two men may grudgingly be forced to offer more concessions to those Catholic Labour MPs who are threatening a Commons revolt.
The Bill is designed to enable research that could lead to significant advancements in the treatment of killer diseases. However, its opponents believe its proposals are ethically wrong and that Catholic ministers should be allowed to exercise their consciences and vote against it.
The outline of the battle is straightforward; the underlying tensions and bitterness that could result from it are more complicated, but are nonetheless vital to understanding what is at stake for Mr Brown's Government as the affair threatens to become one of the most serious crises of his premiership.
The Bill was part of the Prime Minister's first Queen's Speech. It was considered a flagship Bill that would help push the boundaries of medical research and, among other things, hasten cures for illnesses such as motor neurone disease and multiple sclerosis.
However, under its provisions scientists would be allowed to create part-human, part-animal embryos for use in stem cell experiments - a measure described by its more vocal opponents in the Catholic Church as "monstrous". They say such experiments interfere with the sanctity of life.
There are other aspects of the Bill that have outraged its opponents, such as removing the responsibility on IVF clinics to consider "the need for a father", effectively enshrining the concept of two-mother families in law.
But it is the embryo aspect that has caused most angst among Catholic parliamentarians, with Labour MPs reporting bulging postbags on the issue - the vast majority of the letters being from constituents pleading with their member to vote against the Bill.
Labour backbenchers, along with ministers, are being expected to follow Mr Brown's three-line whip - the strict discipline attached to all key Government Bills - to ensure its passage through the Commons. However, already that discipline appears to stand little chance of holding.
Behind the scenes a row has broken out over the vote. At a meeting of Government whips, those who are charged with enforcing party discipline, there has been a significant rebellion.
Big bruising Scottish whips, such as Catholics Tommy McEvoy and Frank Roy, who usually instil fear in Labour ranks, have made it clear they have a problem with being forced to vote for the Bill.
Mr Hoon has been trying to negotiate a solution. After the extent of the disquiet among Government ministers and backbenchers was revealed he said he would allow them to abstain.
While it should be noted that not all Catholic MPs are against the Bill, for many this solution is not enough. They want to be able to exercise their right to vote against it and this is where the real problem lies. Mr Hoon has made the calculation that despite the Conservative Party being largely Anglican, about 80 per cent of Tory MPs would vote against the legislation.
That means it would require only a decent Labour rebellion to stop the Bill passing and that would be a significant blow to Mr Brown's authority and to him personally.
This is an issue Mr Brown clearly cares about. His second son Fraser's illness - he has cystic fibrosis - undoubtedly plays on his mind when people talk about voting against what he sees as vital advances in medicine. Despite being from a religious family he has always believed strongly in science and its benefits.
Unfortunately, a growing number of his own side now seem at odds with him and this weekend's events signalled that the battle is only going to intensify.
# Embryo Bill: What it will mean
Hybrids The Bill would allow the creation of hybrid embryos, where human DNA is inserted into an animal cell for research.
Abortion Amendments to the Abortion Act of 1967 have been included, such as the reduction of the 24-week limit to 20 weeks.
Screening Embryos created during fertility treatment could be screened for genetic diseases but parents would not be allowed to choose embryos that would develop an abnormality, which has angered deaf parents who want a deaf child.
"Spare parts" Embryos could be tested for compatibility with a child suffering a serious medical condition and then implanted into a woman. Stem cells from the new child's umbilical cord, its bone marrow or other tissue (not a whole organ) could be used to treat the ill sibling.
Homosexual couples Such couples who conceive through donated sperm, eggs or embryos would be able to register as parents on a birth certificate and two-mother families recognised.
Rights A child conceived from donated sperm or eggs would be able to seek information about their donor at the age of 16.
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