The Evolution of the Prison: From Rehabilitation to Punishment
While there was an intellectual basis for using prisons as a way to ‘rehabilitate’ prisoners, there were soon major changes in prisons. Due to a series of changes, the prison became a place, not for a criminal to be rehabilitated, but rather, for them to be punished.
Prisons began to change after the Revolutionary War. In Philadelphia, due to prisoners being engaged in hard labor and this causing fear among the populace, people began to form groups such as The Philadelphia Society for Alleviating the Misery of Public Prisons, which argued for prison reform. This push for prison reform culminated in the creation of the Walnut Street prison.
Two major figures involved in Walnut Street were Caleb Lownes and Dr. Benjamin Rush. Rush would eventually become involved in the Walnut Street Prison, but he came into the world of prisons when he went to Europe in 1768 where he “mingled among scientists, philosophers and literati, listening to progressive European theories about such issues as crime and punishment that would eventually follow him to America.”  In Europe he was exposed to the notion that crime was a ‘moral disease.’ This thought would stay with him when he came back to the States and began to argue that crime could be solved by creating a ‘house of repentance’ which would allow for the rehabilitation of criminals.
Once back in the United States, Rush wrote a book entitled An Enquiry Into The Effects Of Public Punishment Upon Criminals, And Upon Society. In it he argued that criminals could not be reformed by public punishments, such as floggings, due to the fact that such punishments “[are] always connected with infamy [and thus destroy] in him the sense of shame, which is one of the strongest out-posts of virtue” and “[are] generally of such short duration, as to produce none of those changes in body or mind, which are absolutely necessary to reform obstinate habits of vice.” Rush’s final argument was that public punishments actually increase crime as “the man who has lost his character at a whipping-post has nothing valuable left to lose” and due to his punishment, the criminal
probably feels a spirit of revenge against t he w hole community whose laws have inflicted his punishment upon him; and hence he is stimulated to add to the number and enormity of his outrages upon society. 
From this manner of thinking he then argued that the only way this situation could be remedied was to fix punishment. He argued that the punishments “if they were moderate, just, and private” and the fact of the certainty of being punished “would lead [the criminal] to connect the beginning of his repentance with the last words of his sentence of condemnation [the length of the punishment].”  In his mind, this goal could be achieved by building “a large house” to hold those who violated the law.
He eventually found a kindred spirit in Ben Franklin and together, along with several others, they established The Philadelphia Society for Alleviating the Misery of Public Prisons in 1787 with the goal being to “substitute public labor for imprisonment, a less costly arrangement than imprisonment while avoiding a return to floggings and dismemberment.” 
Caleb Lownes was a Quaker and began life as an iron merchant and gained immense status in his role of combating an onslaught of yellow fever in 1793. He became involved in prisons when he joined the Philadelphia Society, where he soon became a leading member. The two would eventually become the heads of the Walnut Street prison.
Walnut, being the first prison in America, was quite interesting in its layout as prisoners were held in certain places depending on their crime. In addition to this the layout of the prison, it also served the purpose of attempting to reform prisoners via solitary confinement and hard labor.
Under Lownes, Walnut changed and a wide variety of handicrafts such as shoe making, weaving, and tailoring were introduced to the prison. During his time at Walnut, Lownes wrote a book that stimulated legislatures in other states to reform their criminal codes as “News of the success of the penitentiary house, where convicts were confined to separate cells at night and released to work in the courtyard or shops during the day, attracted a stream of visitors.” 
Another influential figure among the early prison system was Thomas Eddy. Eddy was a merchant and an admirer of the Philadelphia prison reform society and wanted to see those same reforms made in New York. In 1796, he worked with General Philip Schulyer and Ambrose Spencer, two influential politicians in the New York State Senate, to get a bill establishing a state prison passed in the legislature. This bill allowed for several crimes that used to get one the death penalty, to be punished with life imprisonment and made radical changes to the punishment for criminal activity and created different lengths of punishment based on the frequency of the crime. In the book Observations on Penal Jurisprudence and The Reformation of Criminals it reads:
By this law, which has since received several amendments, all those crimes (excepting treason and murder which continue capital) that were before punished with death were punishable by imprisonment for life; all offences above the degree of petty larceny, are punishable for the first offence by imprisonment, for a term not exceeding fourteen years, and for a second offence for life. […] Forfeiture of goods and lands, except for treason, deodands, and corporal punishments, were wholly abolished.  (emphasis added)
The changes are so radical due to the fact that they depart from the traditional thinking of its time where one could be punished either by death, public punishment, or confiscation of goods and land. Instead, it allows for the establishment of a prison and due to these changes in law solidifies the prison as the major means of punishment.
After the bill was signed into law, Eddy became the commissioner of the prison (known as Newgate) and advocated a single cell system in which each convict would be in their own personal cell during the night, but overall followed the Walnut prison model which advocated congregate rooms and workshops.
Eddy advocated this single cell system as “He found, from careful observation, that several [prisoners] confined in a cell corrupted each other, for each one told to his companions his career of vice, and all joined in the sympathetic villainy of to keep each other countenance.”  It was not immediately accepted in New York, but it was implemented in England after Eddy wrote to Patrick Colquhoun as well as Pittsburgh, Pennsylvania. The single cell system was implemented on a small scale in Newgate due to other commissioners being fearful of such a new and untested plan.
However, Eddy’s thinking on prisons would soon change. In 1802, a bloody riot and mass escape attempt took place that was only foiled due to calling in military forces. This caused a shift in Eddy’s view on the structure of prisons. He began to think “that the design of Newgate was a mistake that only an entirely new building could rectify” and that the problem could be solved “with singles cells for the separate confinement of all inmates at night and with shops for their labor in strict silence on weekdays.”  Eddy would eventually resign from his position at Newgate, yet he didn’t give up on prison reform and continued to push his single cell plan. Eventually, it would take root.
In the early 19th century, specifically after the War of 1812, four distinct prison patterns emerged: 1) The solitary system pushed by the Philadelphia Society, 2) A balance between congregate labor and separate confinement with strong discipline, 3) The establishment of separate houses of refuge to take children out of prisons, and 4) The resurrection and reestablishment of prisons to deal with the problem of excess prison populations. These patterns were quite important as they would provide models for prisons to base themselves on for the next 50 years.
In New York, overall population increase prompted a change in the prison system. The establishment of the Auburn Penitentiary was an attempt to handle the population increase. However, even though it had a total of 61 single cells and 28 congregate rooms, this proved inadequate.
Thomas Eddy began to rally support to implement his new single cell plan by forming the Society for the Prevention of Pauperism in New York. In 1822, the group released a book entitled Report on the Penitentiary System in the United States. In it, the group recommended many suggestions that would aid Eddy’s cause, among them that “the internal construction of our penitentiaries be altered,” “when solitary confinement is not adopted, the classification of prisoners be rigidly embraced,” and “that every convict sleep in a solitary cell.”  The group argued in favor of solitary confinement, saying that “Where solitary confinement has been tried, it has produced the most powerful of consequences” and, using examples from prisons in New York and Pennsylvania, stated that even the hardest of criminals “[had], in a few weeks, been reduced, by solitary confinement and low diet, to a state of the deepest penitence.”  Thus, there was in fact evidence that solitary confinement did make it easier for a prisoner to become ‘repentant.’ The state legislature was influenced this evidence and the fact that there was mounting disorder in congregate cells and authorized the implementation of a separate cell system in April 1819.
This creation of a separate cell system changed the structure of prisons and was first implemented in the Auburn prison. William Brittin, the first warden of Auburn, supervised the construction of the north wing which had separate cells. He may have been influenced by the plan of the Ghent House of Correction in 1773 as “on paper [the layout of the prison] appears to show a block of inside cells built back-to-back in one spoke of its octagonal structure.”  “[T]hey were interior cells opening into arcades on each level, but the concept of several tiers of cells opening onto galleries or catwalks could have been borrowed from the 1704 plan for the prison of St. Michael in Rome.” 
Brittin combined both concepts “into a double back of back-to-back cells, each 7 by 3.5 by 7 feet in size, and opening onto narrow wooden catwalks, with the entire five-story cage encompassed by outer walls some six feet distant on all sides from the inside prison grill.”  Yet this designed was changed after a fire occurred when some inmates wrecked the newly built north wing. In order to increase security, Brittin had each cell arched “with brick and topped the block with a cement ceiling 20 inches thick to prevent any access of fire or convicts to the roof.” 
After Brittin’s death in 1821, Gershom Powers became the agent of Auburn and Elam Lynds, the warden. Lynds “was a stern disciplinarian, well-known for his love of freely administered floggings and the summary use of wooden clubs”  and Powers was a very religious man and believed that the prisons needed chaplains to better the morality of prisoners, stating that a resident chaplain which had “a thorough knowledge of mankind; prudent, firm, discrete, and affectionate; activated by motives of public policy and Christian benevolence” would “secure the respect and confidence of a majority of the convicts”  who would consider him as their friend. Under these two, Auburn would evolve as they installed iron grates on cells. This increased the security and affordability of the prison, which attracted attention from the penal authorities of other states.
In addition to this, John Cray, a former Canadian soldier and deputy keeper at Auburn, “devised a strict discipline which included such regulations as downcast eyes, lockstep marching, no talking or other communication between prisoners, and constant activity under close supervision of the guards when [prisoners were] out of the cells.” This discipline, while it kept prisoners occupied for a majority of the day and “contributed to the maintenance of the prison,” also allowed for “an orderly atmosphere that attracted the praise of visitors from other states.”  Due to this “orderly atmosphere,” the same manner of discipline was adopted among other prisons throughout New York.
The prison system changed further with the classification of prisoners. Due to serious outbreaks in the overcrowded Walnut Street Prison, the New York Legislature, in April 1821, ordered the classification of prisoners into three classes: 1) the most hardened criminals who were to be held in solitary confinement in separate cells, 2) the less hardened criminals who were to be held in solitary confinement until they repented, yet they were allowed to work at certain tasks in the day time, and 3) the least hardened criminals who were confined in separate cells at night, but worked in prison shops in silence during the day time.
All of these changes and transformations in the use of prisons revealed “a new determination to use imprisonment as a form of punishment.” 
1: “Eastern State Penitentiary: A Prison With A Past,” Smithsonianmag.com, October 1, 2008 (http://www.smithsonianmag.com/history-archaeology/eastern-state-penitentiary.html)
2: Benjamin Rush “An Enquiry Into The Effects Of Public Punishment Upon Criminals, And Upon Society,” in Basil Montagu, ed., The Opinions of Different Authors Upon The Punishment of Death, vol. 1 (London: Black Horse Court, 1809), pgs 281-282
3: Rush, pg 287
4: Philadelphia Reflections, Pennsylvania Prison Society, http://www.philadelphia-reflections.com/blog/1263.htm
5: Blake McKelvey, American Prisons: A History of Good Intentions (Montclair, New Jersey: Patterson Smith Press, 1977) pg 8
6: William Roscoe Observations on Penal Jurisprudence and The Reformation of Criminals (London: Black Horse Court, 1819) pg 91
7: Freeman Hunt, Lives of American Merchants, vol. 1 (New York: Derby and Jackson, 1858) pg 337
8: McKelvey, pg 9
9: Charles Glidden Haines, Report on the Penitentiary System in the United States (New York: M. Day, 1822) pg 49
10: Glidden Haines, pgs 50-51
11: McKelvey, pg 12
14: McKelvey, pg 13
15: Martin B. Miller, “Sinking Gradually Into The Proletariat: The Emergence of the Penitentiary in the United States,” Crime and Social Justice, No. 14, focus on racism (Winter 1980): 38
16: John N. Miskell, Offering Hope, the Connection between Auburn Theological Seminary & Auburn State Prison, Corrections History, http://www.correctionhistory.org/auburn&osborne/miskell/html/seminary_sabbath.html#copyrite
17: McKelvey, pg 14
18: McKelvey, pg 13