The Unfaithful Deist Racists Versus the Faithful Abolitionists
Another great challenge to the scriptures came through a blend of science and Christianity called deism. Because Isaac Newton claimed there had to be a “first cause” in the physical world, many people reasoned that this must be God, and that his role after creation was to merely wind up the universe like a clock and set it in motion. They argued that he didn’t intervene, so miracles were impossible. This is why Thomas Jefferson, who was a deist, cut all the scriptures referring to miracles out of his Bible and only believed in Jesus as a great teacher.
These “enlightened” men thought that science and empirical evidence were more trustworthy, and should carry more weight than the revealed truth of God’s Word. One result of this refusal to believe in the Bible as the truth was that many Enlightenment thinkers were racists.
Thomas Jefferson, Immanuel Kant, Voltaire, and David Hume, were all “scientific racists” (or polygenists–meaning many origins, or parents). They subscribed to the belief that there was a separate bloodline for each race, allowing for the darker races to be sub-human or of a lower species. As a result, they looked at the different races as though they were merely specimens to be scientifically studied.
For example, David Hume, who was an empiricist (meaning someone who believes that knowledge comes from our senses or the physical realm, rather than from a revelation from God) ascribed a lofty role to the purposes of science.
The sweetest and most innoffensive path of life leads through the avenues of science and learning; and whoever can either remove any obstruction in the way, or open up any new prospect, ought, so far, to be esteemed a benefactor to mankind. 
Yet Hume used science and learning to conclude this:
I am apt to suspect the Negroes, and in general all other species of men to be naturally inferior to the whites. There was never any civilized nation of any other complection [sic] than white, nor even any individual eminent in action or speculation. No ingenious manufactures among them, no arts, no sciences . . . Such a uniform and constant difference could not happen, in so many countries and ages, if nature had not made an original distinction between these breeds of men. (italics added) 
And Immanuel Kant, who, in part, defined Enlightenment thought as the freedom to think for oneself, would make this scientific observation in agreement with Hume:
The Negroes of Africa have received from nature no intelligence that rises above the foolish. Hume invites anyone to quote a single example of a Negro who has exhibited talents. He asserts that among the hundred thousands of blacks who have been seduced away from their own countries, although very many of them have been set free, yet not a single one has ever been found that has performed anything great whether in art or science or in any other laudable subject; but among the whites, people constantly rise up from the lowest rabble and acquire esteem through their superior gifts. (italics added) 
Voltaire, who exemplified the Enlightenment’s emphasis on science and reason, rather than revelation, gives a perfect example of a “scientific” description of a negro specimen:
Their round eyes, their flat nose, their lips which are always thick, their differently shaped ears, the wool on their head, the measure even of their intelligence establishes between them and other species of men prodigious differences. If their understanding is not of a different nature from ours, it is at least greatly inferior. They are not capable of any great application of ideas, and seemed formed neither in the advantages nor the abuses of our philosophy. (italics added) 
Even one of our greatest statesmen, Thomas Jefferson, was a scientific racist. In his Notes on the State of Virginia, he included observations on both Native Americans and blacks. He thought that blacks were inferior to whites because of the way they looked and smelled, and mentioned that they had no ability to plan or give forethought to their actions, were easily aroused sexually, and had no reasoning skills.
He described the negro in scientific language (reticular membrane, symmetry, transpiration, secretion, pulmonary apparatus, principle regulator, etc . . . ) His description is lengthy, so I’ll )just give you a few sentences as an example:
To these objections, which are political, may be added others, which are physical and moral. The first difference which strikes us is that of colour. Whether the black of the negro resides in the reticular membrane between the skin and scarf-skin, or in the scarf-skin itself; bile, or from that of some other secretion, the difference is fixed in nature, and is as real as if its seat and cause were better known to us. And is this difference of no importance? 
The abolitionists cried out against this “enlightened, scientific truth,” saying that it conflicted with the Word of God, which declares in Acts 17:26 (KJV) that he “hath made of one blood all nations of men for to dwell on all the face of the earth.” They proclaimed that all people were descendants of Adam and Eve, and that we were all created “in the image of God.” (Gen. 1:27; KJV)
And yet the greatest scientists of that day flocked to this anti-biblical racial theory. University of Pennsylvania professor, Samuel George Morton, was a polygenist. He also believed in and studied phrenology. This was the concept that skull size and shape could indicate the characteristics of a particular race. His disciples Josiah Nott and George Glidden would write Types of Mankind (or Ethnological Research). Many believers, such as Harvard Professor and geologist Louis Agassiz, embraced polygenism. It was a view supported by most of the major universities and even the American Academy of Arts and Sciences.
Their racial theories contributed to the scientific justification for slavery. According to the Charleston Medical Journal, commenting on Morton’s death, “We of the South should consider him [Morton] as our benefactor for aiding most materially in giving to the negro his true position as an inferior race.” (italics added) 
The addition of science to the Word of God led many Christians to become racists. They never stopped worshiping or loving God, they just added another “truth” to the scriptures, even giving science precedence over the Bible. This led to the corruption of biblical truth and to the vilification of God by future generations, who believe Christians were responsible for the slave trade.
While some Southern slaveholders wrongly pointed to the Old Testament’s “curse of Ham” (Gen. 9:24-27) or biblical admonitions such as “servants, be obedient to them that are your masters according to the flesh” (Eph. 6:5; KJV) as justification for having slaves, other Christians used the authority of the Word of God to confront slaveholders and try to persuade them to let go of their slaves.
In reality, if Southern slaveholders had obeyed the scriptures, there could have never been a slave trade. Both the Old and New Testaments forbid kidnapping and selling people.
And he that stealeth a man, and selleth him, or if he be found in his hand, he shall surely be put to death. (Exod.. 21:16, KJV; italics added)
Knowing this, that the law is not made for a righteious man, but for the lawless and disobedient, for the ungodly and for sinners, for unholy and profane, for murderers of fathers and murderers of mothers, for manslayers, for whoremongers, for them that defile themselves with mankind, for menstealers, for liars, for perjured persons, and if there be any other thing that is contrary to sound doctrine. (1 Tim. 1:9-10, KJV; italics added)
In order for the slave traders to obtain people for their business, they had to force them to come to America against their will. And in order for the Fugitive Slave Act to be enforced, the slaveholder had to violate the scriptures, which forbids a slave to be held against their will.
Thou shalt not deliver unto his master the servant which is escaped from his master unto thee: He shall dwell with thee, even among you, in that place which he shall choose in one of thy gates, where it liketh him best: thou shall not oppress him. (Deut. 23:15-16, KJV; italics added)
Not only did the southern slaveholder violate the letter of the law, he also violated the spirit of the law. After all, Jesus said he came to “preach deliverance to the captives” (Luke 4:18; KJV), and the great miracle of the Old Testament was the deliverance of the Jews out of the bondage of Egypt.
Battling against polygenism were the abolitionists who stood on the Word of God. They were known as monogenists. Evangelicals in London, for example, set up the Aborigines Protection Society in an attempt to protect the darker races from the abuse of British colonizers. The opening page of William Howitt’s expose, Colonisation and Christianity, quotes the prophet Malachi:
Have we not all one Father? Hath not one God created us? Why do we deal treacherously one man against his brother? (Mal. 2:10; KJV)
Out of this group, another organization, known as the Ethnological Society of London, would form with the express purpose of battling scientific racism. Their motto, ab uno sanguine (from one blood), would counter polygenist views o the origin of humanity. Its membership included many from the Clapham Sect, a group of evangelicals who worked with William Wilberforce to successfully abolish slavery in the British Empire. John Newton, author of the great hymn “Amazing Grace,” was a former slave trader who came to Christ and worked as an ally in their cause.
In America, the former slave Frederick Douglass would also battle against scientific racism. He sarcastically referred to the polygenists, Morton, Glidden, Nott, and Agassiz, as a “phalanx of learned men” and gave a speech at Western Reserve College in 1854 entitled “The Claims of the Negro, Ethnologically Considered,”  in which he attempted to refute polygenism and its supporters. He asked his listeners to judge the truthfulness of a scientific theory based on what kind of fruit it produced in society, and whether it brought glory to God.
Some atheists point to the antislavery views of the skeptic Thomas Paine as evidence that unbelievers were also on the right side of history, but Paine based much of his abolitionism on the teachings of the scriptures, reminding Christians that they were to love their neighbors and that “man-stealing” (kidnapping) was a sin. 
The ultimate push needed to abolish the slave trade came from the effects of the Second Great Awakening. According to historian Dwight Lowell Dumond, a University of Michigan professor who specialized in studying the antislavery movement, “evangelicalism and the antislavery movement were inseparable.” He said that the “evangelistic movement, particularly Finney’s revival, provided a host of young men dedicated to preaching the Gospel” and gave the antislavery movement “an unprecedented number of devoted apostles” who, as intellectuals, would be “the greatest combination of moral and intellectual power ever assembled in support of any cause before or since.” To help them in this endeavor, Dumond says this:
They had the Bible. They had the great charters of Western liberalism. They had the writings of Woolman, Benezet, Rush, Hopkins, Cooper, Rice, Branagan, Barrow, Duncan, Rankin, and a host of British liberals such as Sharp, Clarkson, and Wilberforce. They needed all of this and more to beat down and destroy the doctrine of racial inequality, enshrined in slavery, and upheld by the courts, the churches, and the political parties. (italics added) 
Many Christians, such as Harriet Tubman, were conductors on the Underground Railroad. Believers would also redeem slaves, just as the early church, purchasing them and setting them free.
William Lloyd Garrison, the great abolitionist, would publish ads in his newspaper, The Liberator, in which former slaves would ask for financial help in redeeming their children from slavery. The abolitionists were mocked, tarred and feathered, and persecuted, but they are now considered to be some of the greatest heroes of history.
There were two groups of believers involved in the battle over slavery. One group heroically stood fast on the Word of God, and the other group disobeyed and compromised the Word with the latest scientific views. One group was faithful to God and loved and cared for their neighbor; the other group corrupted the Word by adding scientific “truth,” which countered the scriptures, to their Christian beliefs.
Consequently, when the polygenists compromised biblical truth, they betrayed humanity. Their false views were used as a justification for human bondage and cruelty. The slaveholders may have called themselves Christians, but they were actually spiritual adulterers and hypocrites who were disobedient to the commands of God. Worst of all, their actions have caused the name of Jesus to be blasphemed even to this day.
 David Hume, An Enquiry Concerning Human Understanding: A Critical Edition, ed. Tom L. Beauchamp (Oxford: Oxford University Press, 2000), 8-9.
 David Hume, The Philosophical Works of David Hume, cont. Henry Maudsley (Boston: Little, Brown, and Co., 1854), 228.
 Immanuel Kant, “Observations on the Feeling of the Beautiful and Sublime,” quoted in David Brion, Inhuman Bondage: The Rise and Fall of Slavery in the New World (New York: Oxford University Press, USA, 2006), 75.
 Voltaire, “Essai sur les mouers,” quoted in David Brion, Inhuman Bondage: The Rise and Fall of Slavery in the New World (New York: Oxford University Press, USA, 2006), 75.
 Thomas Jefferson, Notes on the State of Virginia (Richmond, VA: J.W. Randolph, 1853), 149-150.
 Crispin Bates, “Race, Caste, and Tribe in Central India: the early origins of Indian anthropometry.” In Peter Robb, The Concept of Race in South Asia (Delhi: Oxford University Press, 1995), 225.
 William Howitt, Colonisation and Christianity: A popular History of the Treatment of the Natives by the Europeans in All Their Colonies, 1838 (Whitefish, MT: Kessinger Publishers, 2004), 1.
 Frederick Douglass, “The Claims of the Negro Ethnologically Considered,” An Address Before the Literary Societies of Western Reserve College, At Commencement, July 12, 1854, The Frederick Douglass Papers, 10, The Library of Congress, accessed Feb. 16, 2015, http://memory.loc.gov/cgi-bin/query/r?ammem/rbaapc:@field(DOCID+@lit(rbaapc07900div2)).
 Thomas Paine, “African Slavery in America.” Pennsylvania Journal and the Weekly Advertiser, March 8, 1775. Accessed February 16, 2015. http://constitution.org/tp/afri.htm.
 Dwight L. Dumond, Antislavery: The Crusade for Freedom in America (New York: W.W. Norton and Co. Inc., 1961), 158-159.