Logic and Critical Thinking in the Biomedical Sciences

1. Introduction to biomedical logic Section 1.1. What is reasoning? Section 1.2. What is proof? Section 1.3. Fallacies Section 1.4. Can several weak arguments substitute for one strong argument?

2. Drawing inferences from photographs Section 2.1. Thinking about what we see Section 2.2. Looking at nuclei Section 2.3. Deducing that the chloroplasts in plant cells are captured cyanobacteria Section 2.4. Phylogenetic advances manifest themselves in the embryo Section 2.5. All eutherian cell types are equivalent among classes of speciesSection 2.6. Length of gestation in eutherian animals Section 2.7. Inferring that there are many more than 200 cell typesSection 2.8. What we learn from looking at red blood cellsSection 2.9. What we learn from inclusion bodies

3. Inferences drawn from organismal development Section 3.1. Desmosomes, the essence of animals Section 3.2. Ear ossicles missing from reptiles Section 3.3. The wisdom of teeth Section 3.4. The development of bones Section 3.5. Unnecessary cerebellum Section 3.6. Mammalian hair and the origin of basal cell carcinoma Section 3.7. Inferences drawn from the shape of snake heads Section 3.8. Depth of penetration of ultraviolet light Section 3.9. Evolution is often a one-way road

4. Inferences drawn from temporal sequences Section 4.1. Paradoxes of creation Section 4.2. A logical approach to bootstrapping paradoxes Section 4.3. Inferences drawn from the sequence of clinical events preceding death Section 4.4. When was aging invented? Section 4.5. When does aging begin? Section 4.6. Old age does not cause cancer Section 4.7. What can we infer when we know the time at which a mutation occurred?

5. Finding relationships among biological entities Section 5.1. Defining relationships and similarities Section 5.2. Ancestral genes Section 5.3. The significance of gene sequence conservation Section 5.4. Unexpected gene conservation Section 5.5. Relationships between human diseases and orthodiseases Section 5.6. Inferring the relationships between genetic diseases and their phenocopiesSection 5.7. The logic of treating disease pathways, not disease genes

6. Drawing inferences from classifications and ontologies Section 6.1. What is a classification? Section 6.2. Ontologies Section 6.3. Some paradoxes of classifications Section 6.4. The classification of living organisms and the meaning of “species”Section 6.5. Speciation is the primary driver of evolution Section 6.6. Classifications allow us to discover class-specific treatments of diseases

7. Biomedical advances achieved by reducing class noise Section 7.1. Significance of class noise Section 7.2. Why fungi are definitely not plants? Section 7.3. Naegleria fowleri is not an amoeba Section 7.4. Clinical trials for staged cancers Section 7.5. Psychiatric illnesses Section 7.6. Cures for the most common and chronic diseases Section 7.7. The mistake of overclassifying in an effort to avoid class blending

8. How a little logic could have corrected long-held misbeliefs Section 8.1. We should have known better Section 8.2. An embryo is not a miniature baby Section 8.3. The genome is a recipe book, not a blueprint Section 8.4. Why our genome is full of junk Section 8.5. Bacteria live in our stomachs Section 8.6. We can abandon Koch’s postulates Section 8.7. Diseases arise through a sequence of events that occur over time Section 8.8. The egalitarian nature of logical analysis