Freedom of conscience
Freedom of conscience is the right of people to believe and act in accordance with their personal values and beliefs. It is closely related to the concept of freedom of religion. It is debatable if such a right exists and the extent of the protections it affords. Freedom of conscience has also been defined as:
- "men should act on their own judgment, enjoying and making use of a responsible freedom, not driven by coercion but motivated by a sense of duty "
It stipulates that people should not be forced to perform actions that they find immoral, particularly in the context of "coercion in civil society".  It is sometimes cited by believers in cases involving abortion, contraception, homosexuality, religiously motivated medical neglect, same sex marriage and military drafts. It is controversial because this right arguably puts actions that are motivated by religion above secular law. Apologists argue that the right is necessary for freedom of religion to be meaningful.
Some countries and jurisdictions provide legal protection for freedom of conscience. Canada provides constitutional protection.  Various US disallow laws that "substantially burden" the exercise of religion, unless there is a compelling interest. 
Some Christians withhold their services to certain groups because of their disapproval of that group. For instance a bakery in Northern Ireland refused a cake order for a gay couple because it was at "odds with what the Bible teaches".  A guesthouse in England turned away a gay couple because of a "religiously-informed judgment of conscience".  This is not very like racist shop owners refusing to serve foreigners or ethic minorities. The only difference is one is a non-religious personal choice, the other is a religious personal choice. From secularism, it is undesirable for a society to consider religious beliefs as superior to non-religious personal preferences.
Some marriage clerks in the US are refusing to issue marriage license to gay couples, despite this being one of their job's duties. 
A conscientious objector is a person that refuses a military draft on religious or ethical grounds. In some cases, it can be difficult to establish this status unless a person is a member of certain religious groups. In the UK, the Militia Ballot Act of 1757 exempted Quakers from military service based on their long standing pacifism.
Some US employers opt out of providing contraception?
Narcotics in religion
- Main Article: Entheogen
Narcotics are used an many religions, either historically or in modern times. While the use of many narcotics are illegal in many countries, some grant exemptions for religious use. The US has the legal principle of the Sherbert Test, which allows some traditional use of narcotics in religious practices. This places religious beliefs in a special category that is above secular beliefs, which violates the principle of equal regard.
Employment and holy days
Some theists want to avoid employing atheists:
- "You know there is a lot of reasons why Christians or Jews might not want to hire an atheist. In fact it's in the New Testament. It says things such as 'avoid them', 'disassociate with them', in Romans, Thessalonians, Corinthians. You might want someone who believes in a higher power, for example maybe you are running an airline and hiring pilots and maybe you prefer they believe in Hell. I know that sounds extreme but that shows you why religion is so important, to so many people. To tell people you can't hire only people of faith intrudes on their free exercise of their faith. "
In the United States, Sherbert v. Verner was significant in determining the way freedom of conscience is handled. A Seventh-day Adventist was changed from a five day to a six day working week, including Saturday. Since they considered working on Saturday to be working on the Sabbath, she refused to work and was subsequently fired. She applied for unemployment benefit and was denied. The legal challenge progressed to the US Supreme court, while ruled that denying her belief was an "unconstitutional burden on the free exercise of her religion". The dissenting opinion pointed out this ignored potential secular beliefs such as Saturday (or any other day) should not be a day of work, which is either unfair or an absurd conclusion to reach.
- "The State, in other words, must single out for financial assistance those whose behavior is religiously motivated, even though it denies such assistance to others whose identical behavior (in this case, inability to work on Saturdays) is not religiously motivated. It has been suggested that such singling out of religious conduct for special treatment may violate the constitutional limitations on state action. [...] Those situations in which the Constitution may require special treatment on account of religion are, in my view, few and far between"
The court's ruling gave rise to the Sherbert test, which prevented any substantial burden on the exercise of religion unless there was suitable justification for such a burden.
Some theists wish to wear religious clothing, even when their employment normally requires a uniform.
Female genital mutilation
State licensed discrimination
Freedom of conscience effectively legitimises discrimination against minority groups, such as homosexuals.
"[laws] should not be changed to permit individuals to opt out of work duties, to accord with their religious or non-religious beliefs, where this has an actual or potential detrimental or discriminatory impact on others"
- — Equality and Human Rights Commission
- "It’s more of a freedom to discriminate bill rather than a freedom of religion bill "
"These bills rationalize injustice by pretending to defend something many of us hold dear. They go against the very principles our nation [the United States] was founded on, and they have the potential to undo decades of progress toward greater equality. [...] I was never taught, nor do I believe, that religion should be used as an excuse to discriminate."
- — Tim Cook, Apple CEO 
"This bill is not about discrimination and if I thought it legalized discrimination I would have vetoed it."
Incompatible with more fundamental rights
Freedom of conscience is contrary to a society based on laws that are written by just law makers and apply generally for the purposes of regulating society.  If people can opt-out of laws based on their personal beliefs, the entire system is unworkable. In contrast to granting exemptions to laws based on religious belief, a better redress for unjust laws is their replacement by better laws that apply generally.
Competing contradictory beliefs
There are many religions and they have diverging incompatible views on some subjects. It is impossible to allow freedom of conscience without denying it to another. Arguing for freedom of conscience is a broken compass argument.
"When individuals cannot allow their religious loyalties to be trumped by their public responsibilities, they should resign; the alternative is for the public domain to be invaded and disrupted by a Babel of claimed individual religious sensitivities, or even worse, by various religious organisations whose prejudices, taboos, anxieties and antipathies distort the overall public endeavour for a decent and equitable social order which is as inclusive as possible."
Criticism from religious quarters
Various religious leaders have argued against legal protection of conscience.
- "Our perspective is that hate and bigotry wrapped in religious freedom is still hate and bigotry "
- "It uses religion in a way that actually spreads hate rather than love "
- "This bill is a solution in search of a problem "
Cherry picking which groups to discriminate against
Theists often cherry pick which groups to discriminate against without any consistency. For example, certain Christian shop owners refuse to serve gay customers but would serve an adulterer. They argue that adultery is a "different kind of sin", which is special pleading. 
The Bible says Christians will be persecuted
"All who desire to live a godly life in Christ Jesus will be persecuted"
In various US states, including Massachusetts, driving license photos are banned from having hats or head wear except for those worn for religious reasons. Various people have used this exemption to wear a pastafarian colander in their head for their driving license photo.  Since the religion is generally considered a satirical believe system, this action is probably intended to point out the absurdity of religious exemptions. Having religious beliefs privileged above secular motivations, such as fashion or head warmth, is a violation of church-state separation.
- ↑ 1.0 1.1 
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- ↑ 3.0 3.1 
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- ↑ Anti-Gay Marriage Clerks Won't Do Their Jobs
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- ↑ female genital mutilation is a religious right claim lawyers in first US case on the practice
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- ↑ 10.0 10.1 10.2 
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- ↑ Richard J. Arneson, Against Freedom of Conscience, 2010
- ↑ A. C. Grayling, Prejudicial concerns, The Guardian, 23 October 2007
- ↑ The Young Turks, Religious Bigot Against Gays But Adultery Is A “Different Kind Of Sin", 3 Apr 2015
- ↑