While Jefferson waxes rhetorical with observations about slavery and 
speculation about black physiology in the "Laws" section of 
Notes on the State of Virginia,
 the "Manners" section seems to give a snapshot of his actual judgement 
about slavery. He fears that the wrath of God will come down on the new 
Republic and observes "The spirit of the master is abating, that of the 
slave rising from the dust" (p 175).
Returning to the "Laws" 
section of the text, we see Jefferson's observations about the very 
nature of blacks. While our essay prompt mockingly refers to 'science', 
this 
was cutting edge science for Jefferson and his 
contemporaries and these were serious concerns of the day.  Jefferson 
proffers many differences between blacks and whites, not only 
"political", but also "physical and moral" (p 149). He argues that upon 
the emancipation of the blacks in the Republic, they should be given a 
fresh start in a new land and be replaced by white immigrants; they 
cannot be incorporated into the Republic due to "Deep rooted prejudices 
entertained by the whites" and "ten thousand recollections by the blacks
 of the injuries they have sustained" (p 149). He goes on to delineate 
ways in which blacks are different from (read: inferior to) whites in 
their most basic attributes. He remarks that they are less attractive 
than whites, their bodies process waste differently from whites, giving 
them a "strong and disagreeable odor" but also makes them "more tolerant
 of heat, and less so of cold than whites" (p 150).  Jefferson continues
 by stating that blacks require less sleep, use less forethought, and 
are more ruled by sex than romance than whites. In fact, he summarizes 
nicely for us his position when he says "In general, their existence 
appears to participate more of sensation than reflection" (p150).
The
 modern reader at this point is tempted to raise a query at this point -
 what about blacks who were not slaves, or who became free and gained an
 education?  Here Jefferson compares the idea of an educated black 
writer to a white one: "though we admit him to the first place among 
those of his own color who have presented themselves to the public 
judgment ....when we compare him with [a white writer] we are compelled 
to enroll him at the bottom of the column" (p 152).  Jefferson does not 
waver from his theory of black inferiority, even citing 
examples of enslaved whites who were far "smarter" than his contemporary
 enslaved blacks in America, and under supposed far harsher conditions 
(p154). Clearly he does not support the idea that slavery itself is the 
problem here. 
For Jefferson, the only way that the idea of 
emancipation could be entertained was by putting forth the idea of 
removing all freed blacks from the American (white) Republic. He again 
contrasts the American situation to that of ancient Rome:   Among the 
Romans emancipation required but one effort. The slave, when made free, 
might mix with, without staining the blood of his master. But with us a 
second is necessary, unknown to history. When freed, he is to be removed
 beyond the reach of mixture." (p 155).