The Prime Minister announced a partial free vote on the government side in a recent compromise over 'conscience' issues in the Bill, which includes strictly limited provision for research into deadly diseases using tiny admixed embryo cells.
The Catholic Church opposes any human embryo research, saying that the cells have the moral status of a human person. Other churches and religious groups take a different view, though there is widespread disquiet about the drift of such research among faith groups.
Cardinal O'Brien has been on holiday since likening the use of microscopic animal cells to 'Frankenstein" like research, a comment which provoked accusations of telling untruths from Lord Winston and senior scientists.
However, a spokesperson for the Cardinal said on BBC Radio 4 two days ago that he would be making a speech in Gordon Brown's parliamentary constituency today, emphasising his continued opposition to the legislation and saying that the concession on voting was not enough.
Supporters of the Bill have accused the Cardinal and others in the churches of bullying and misrepresenting to get their way.
MPs will now be able to follow their individual consciences in three areas - including allowing scientists to create embryos with human DNA and animal cells.
But the PM says he expects all Labour MPs to back the whole bill when it comes to the final Commons vote.
Gordon Brown offered the deal after warnings that some Catholic Labour MPs and cabinet ministers were ready to rebel. Others have accused him of a 'sell out'.
Liberal Democrat and Tory MPs had been offered a free vote at all stages of the Bill, and some political reformers argue that there should be more open voting in parliament and less control by the party whipping system.
The Human Fertilisation and Embryology Bill come 18 years after previous legislation in the area, and after a two-year debate.
It has the backing of the General Medical Council, science research bodies and the Human Fertilisation and Embryology Authority - an expert panel that includes former Anglican Bishop of Oxford Lord Harries.
A number of faith and anti-abortion groups have vociferously opposed it.
The Association of Medical Research Charities says that although there are ethical issues in allowing scientists to create embryos that combine human DNA and animal cells for research, the move presently under consideration is strictly controlled and offers "considerable benefits" to future patients.
In a letter to the PM the network of 200 charities goes on to say the charities believe there is considerable public support for the move.
The letter states: "... public understanding of the importance of the use of early-stage embryos and ensuing stem cell research remains robust; there is a real acknowledgement of its potential for those who are ill."
Simon Barrow, co-director of the Christian think tank Ekklesia says that in reality opinion within the churches and other religious communities is divided both on the current Bill and on the longer term prospects of research in the biosciences.
But he described Cardinal O'Brien's rhetoric as "inflammatory and unhelpful", adding that it has "further politicised a debate that needs to be thoughtful and rational."
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