On this high shelf a whole series of enormous bundles of papers were arranged in order, methodically classified. Here were papers of all sorts: sheets of manuscript, documents on stamped paper, articles cut out of newspapers, arranged in envelopes of strong blue paper, each of which bore on the outside a name written in large characters. One felt that these documents were tenderly kept in view, taken out continually, and carefully replaced.

Doctor Pascal is described as being generally untidy in his personal life and appearance but, in contrast, extremely neat (almost obsessive) when it comes to maintaining order in the space where he keeps the papers that chronicle and record his scientific research. Although Clotilde helps him with his work, which he expects will soon result in a book, only he is allowed to touch these papers. His attitude toward these papers plays an important role, as he clashes with his mother over her concern that they hold family secrets (including information on a family member's insanity), which she believes should be destroyed.

Heredity, instead of being resemblance, was an effort toward resemblance thwarted by circumstances and environment. And he had arrived at what he called the hypothesis of the abortion of cells. Life is only motion, and heredity being a communicated motion, it happened that the cells in their multiplication from one another jostled one another, pressed one another, made room for themselves, putting forth, each one, the hereditary effort; so that if during this struggle the weaker cells succumbed, considerable disturbances took place, with the final result of organs totally different.

The clash between religion and science is also a strong theme in the book. This is mostly characterized by the conflicts between Dr. Pascal and his mother. In part because of the presence of mental illness in their family, Dr. Pascal devotes himself to research on heredity. He is searching for explanations for what he calls the "accidents" (equivalent to the mutations that occur in genetics) that make children depart from exact resemblance to their parents.

You remember how you crushed me in your grasp. It left a bruise, and a few drops of blood on my shoulder. Then your being entered, as it were into mine. We struggled; you were the stronger, and from that time I have felt the need of a support. At first I thought myself humiliated; then I saw that it was but an infinitely sweet submission. I always felt your power within me. A gesture of your hand in the distance thrilled me as though it had touched me. I would have wished that you had seized me again in your grasp, that you had crushed me in it, until my being had mingled with yours forever.

Another central idea in this work is the tension between logic and passion, evident in the incestuous relationship between Clotilde and Dr. Pascal. As Clotilde enters adulthood, her future is in question. Her brother, Maxime, wants her to live with him in Paris. However, she has received a proposal from another physician—the handsome young Doctor Ramond. Telling him that she is worried about her uncle, whose health has been suffering due to overwork and anxiety, she hesitantly accepts him. The realization that Clotilde will be leaving him pushes Dr. Pascal into a bout of serious illness, as he has recently been tormented and conflicted by his sexual attraction toward her.

During Dr. Pascal's illness, Clotilde nurses him. After he recovers, Clotilde comes to realize that it is Dr. Pascal, not Ramond, whom she loves. She then calls off the wedding. When Dr. Pascal demands to know why she did this, she brings up an incident when she had confronted him about the dangers of his scientific research which could reveal all the family's secrets, which included incest. She declares that this night, described in the quote above, was the turning point at which she realized her love for him.