1. Are genes signs and if so what are they signs of? John Collier Philosophy, University of KwaZulu-Natal, Durban 4041 South Africa collierj@ukzn.ac.za collierj@ukzn.ac.za http://web.ncf.ca/collier This work was partially supported by the South Africa National Research Foundation

2. Outline What is a gene? What do genes do? Genetic transmission – Internal (somatic) – External (heredity) Proteins as gene reference Traits as gene reference Environmental factors as gene reference

3. What is a gene? Mendelian genes are hereditary units that determine traits. DNA genes were originally thought to determine traits, once DNA was discovered to be the hereditary material. But discovery of the genetic code led to the idea that they determine proteins: DNA → mRNA → Protein. Even this is too simple due to RNA editing, methylation, and other factors. The same units of DNA can map to different proteins, for example. Many DNA units are regulatory, and many others have no transcription (junk DNA).

4. Problems with the gene-trait view Other factors are also inherited (but usually secondary). These are typically called “epigenetic”, suggesting they are really grounded in genes. Aspects of human culture are included. Arguably this is at least as important as out genetic heritage. So, genes can no longer be thought of as the hereditary unit that determines traits. This is especially so since there are largely independent channels of heredity (esp. culture in humans and other animals). Furthermore, genes work together and also regulate each other, and cannot be treated separately. This undermines the gene-trait relation.

5. So what does the genome do? An inherited blueprint for the organism. An inherited program (code)for producing an organism Some biologists reject the program description of DNA, and say that the program is in the soma. DNA in this case is inherited data. Whether blueprint or data, it is fair to ask “blueprint of what?” or “what do the data stand for?” The remainder of this talk addresses these questions.

6. Blueprints and programs A blueprint in the DNA is a metaphor. A blueprint of a building is a model of the finished building, but the DNA is not a model of the organism. A set of interacting traits is more similar to a blue print. The DNA is also not a program, though it might be thought to contain instructions on how to form an organism. The soma would then be the processor, but it does not have the mechanical properties of a processor, and it adds new features as the organism develops, unlike a computer.

7. Problems with genetic code model 1.RNA editing, already mentioned, undermines the DNA-gene-trait relation. 2.Methylation can be hereditary, hence a Mendelian gene, but not a DNA gene. 3.Transcription process of DNA to proteins can be understood chemically, so it is not clear that talk of reference is either required or makes sense. Another way of putting this is that there is no Peircean object. 4.Genetic code suggests a protein reference, but does not answer “Why genes?” For this we need to consider the functionality of the genetic system within its proper context. Code only explanations are incomplete and don’t distinguish between biological processes and what might happen in a test tube. Again, any reference here is not a Peircean object. 5.The code model ignores heredity and selection on lineages, and hence ignores the important role of environmental influences on gene propagation. These environmental influences can also affect the development of individual organisms, so there is no simple DNA-trait code.

8. DNA as data The idea here is that the DNA serves as data for a somatic program. Again there is no notion of functionality involved, and the process could be the same as in a test tube. This questions whether the DNA has an object (reference). Furthermore, there are two possible references even if we allow this idea: 1) organism traits, 2) environmental factors that allow traits to be functional.

9. DNA as information Using the formal channel ideas of Barwise and Seligman it is possible in principle to explain how DNA is expressed in traits and their interactions (Collier 2008). The method permits an information channel between different things under different classifications. However not all DNA is so expressed, and this DNA as no object, at best. Nonetheless, the method allows a connection between expressed DNA and organismic traits. However the method is not enough to give meaning to the genes, since the information is purely syntactic.

10. Autonomy and function I have argued that the identity of the organism is given by its autonomy. This is the set of traits that contribute to its survival. I argue that a trait, and hence whatever DNA is expressed informationally in the trait is thereby functional, and interpreted by the organism autonomy. This gives a meaning for the organism of the trait. This gives a Peircean object via the final interpretant for the expressed DNA.

11. Functionality and environment Functionality, and autonomy, however, depend on likely organism environments. Thus the environment is also expressed in the autonomy, and retrospectively in the DNA data. We must assume, therefore, that there are two possible objects for DNA data: organism traits and environmental properties.

12. Ontogeny and phylogeny Traits are produced ontogenetically in the individual organism. Environmental influences, however, are produced through selection of the more functional traits through environmental properties. This function preserves the lineage, giving a meaning with respect to lineage preservation. It is only retrospectively that these properties play a role in the individual organism.

13. Two kinds of objects; two interpretants I propose that we must consider two interpretants, one related to the formation of the traits of the organism from DNA data, and the other producing the DNA data through the process of selection. These two interpretants give different objects for the DNA data, traits and environmental properties. These are not contradictory, but are in fact complementary.

14. Thank you John Collier http://web.ncf.ca/collier