In the spring of 1856, members of the VMI Society of Alumni responded to mounting criticism of Jackson's teaching skills. They presented to the Board of Visitors a petition to have Jackson removed from office, which the Board promptly tabled without discussion. Jackson was unaware of this controversy until a year later, and no action was ever taken by the Board. Superintendent Francis H. Smith, in an attempt to look objectively at the controversy, contacted James T. Murfee, a respected graduate who stood first in his class in 1853 and had studied under Major Jackson. Murfee was employed as a professor of mathematics at a college in Lynchburg, Virginia.

August 7, 1856. Excerpt, Murfee to VMI Superintendent Francis H. Smith

"...The matter of Maj. Jackson's Professorship was brought up on the morning of the 4th [July], by a very worthy member of the Alumni, he being actuated as I supposed and feel assured of, by the same motives of interest in the Institute as I was in all I did and said. And in all this matter I wish to be understood as having the greatest regard for Major Jackson as a man--such regard, indeed, as would make it, as it is, a matter of very great regret to me to say or do anything that would ever tend to injure his feelings; for I give him credit for all the good qualities that you do. Now at the same time that I have these opinions of him in regard to the purity of his motives, I know that he did not, nor has not done as far as I can learn, anything like justice to his department, and from the same opinion on the part of many, it seems that the Institute is suffering much; indeed, but for this consideration, and my acquaintance with him as a Professor, I should not have been in favor of the action of the Alumni, but as it was, I was much in favor of it, and desire the evil may be remedied with as little injury to Major Jackson and with as much credit to the VMI as possible; and this was expressed as the desire of the Alumni.

You are pleased to refer to my success to prove that the Alumni are mistaken in their views. But a reference to the many difficulties I have had to contend with in my experience, proves most conclusively that I was less prepared to teach Nat. Philosophy than anything else, and it has been the greatest task I ever had, to save my reputation and that of the Institute; and if I have succeeded in it, it has been only by dent of study and application, that have cost me a great deal of health and capital.

You seem to conclude that my preparation in Nat. Philosophy was as good as that in Mathematics; but Sir, allow me to say, that in so far as any qualifications to be Prof. of these Departments, there is was no more comparison, than there is between the merest tyro in any study and the best scholar. You, Sir, are Prof. of Math and knew my qualifications for this chair, but you knew very little if anything, in regard to my qualifications to teach Nat. Philosophy.

As to the importance of the use of instruments in teaching Natural Philosophy....I would about as soon study watch-making without a watch and instruments, as I would study, as I did at the VMI, Nat. Phil. without an apparatus....When an apparatus is at hand, there is no excuse for a Prof. if he does not give his classes the use of it, be the labor what it may....You consider it very important to have your classes instructed in the principles and use of Mathematical Instruments, and certainly this is not so important as the whole course of Philosophical Instruments.

You think Maj. Jackson is improving, and so do I think he has done and is doing all he can, but if he could ever make himself capable of filling that chair as it should be then I know no principle, by which to judge of a man's talents. All this I can say without great discredit to Maj. J., for in such an Institution as yours, it requires much more than an ordinary man--such a one as has very few if any superiors in the country. In this day of science the Chairs of Chemistry and Natural Philosophy are the most important; and I want to see the VMI leading the country in these things, and I am pleased to know she is, or bids fair to do it in the Department of Chemistry. The VMI has directed the attention of the country towards herself on acct. of the superiority of her Profs. of Math, and some kindred subjects, and in connection with these the learned world expects great merit in the department of Natural Philosophy. Now unless this merit can be seen, the Institute must suffer beyond any calculation.

I have now availed myself of saying to you about all I have ever said, and that I have said only in the meeting of the Alumni. It was the expressed understanding in that body that this thing was to be managed as delicately as possible. I would blush to make such facts known to strangers. Had I had no interest in the VMI, I should for personal consideration, wish to consign such thought as these to oblivion as possible.

Maj. Jackson has been, I suppose, informed of these things by authority of the Alumni, and hence as a member of that body, I can express to you my views as presented to the Alumni. You may, if you deem it necessary, show him this communication, for although I am anxious to save his feelings and reputation, I say or do nothing against a man that I am not perfectly willing an anxious for him to know. I did what I thought my duty and now I rest perfectly contented to leave the matter to proper authority; for as I said before, on account of personal respect, I shall say no more of a subject so disagreeable to think of."