Genes and Phenotype
We are constantly seeing both news articles as well as scientific publications on new genes - the new gene for intelligence, cancer or happiness. So lets start at the beginning by figuring out what a gene is. Simply, its a way to refer to inherited traits.
There are a wide variety of traits that are controlled by genes. Flower color is a pretty obvious trait, so lets use a flower that comes in both white and red as an example. We call the specific variety of a trait that an individual has the phenotype. So there is a gene that is responsible for flower color and an individual can have a phenotype of white or red.
However, not everything is predetermined by genes. Brushing your teeth isn’t due to a gene, but is taught to children by their parents. So for something more complex like intelligence, how can we tell if its a gene or something else? It may seem circular, but by looking at if its inherited - are you more like those who are biologically related to you than to others. This becomes even clearer if you look at adopted individuals (called cross-fostering experiments in animals) who should have the trait of their birth parents if the trait is inherited. We would call this a genetic trait.
Once upon a time, biologists hoped that every inherited trait had a single gene that was responsible for all the various phenotypes. However, we now know that some traits like intelligence are influenced by both the environment and genes. Other traits like hair color or height are controlled by multiple genes. A lot of modern biology experiments, in fact take advantage of the fact that its not as simple of 1 gene = phenotype.
You might have noticed that I have not discussed DNA in defining a gene. Thats because for a most biological experiments, the basic unit is the gene. We are interested in understanding how a gene leads to a phenotype - i.e. how it is regulated.
When a gene is identified as playing a role in a trait, this can be caused by basically two things - 1) different versions of a gene called an allele or 2) changes in how or where a gene is used. To understand how genes can give rise to different traits, we need to first understand how a gene functions.
First, let us expand upon our earlier definition of genes. They are inherited traits that are represented by a specific stretch of DNA. Therefore different alleles represent different sequences.
I will note that not all differences in sequences result in a functional change, but most alleles that get mentioned do. Some alleles are functionally the same - for instance, there can be multiple correct ways to spell a word (grey vs. gray) but it doesn’t change the word’s meaning. Some alleles have minor changes that make a big difference - just like some words sound the same but have very different meanings (sun vs. son).1
Changes in how or where genes are used is called expression differences. We can look at these differences in anything from a single cell all the way to a whole organism.
The types of sequence changes that make allele’s different are called polymorphisms. ↩