Phenotype: A scientific word explained with examples from a 3 year-old

Today is a genetics vocabulary lesson on the word phenotype. It’s a rather large word that biologists like to use. Below is the definition from

(1) The physical appearance or biochemical characteristic of an organism as a result of the interaction of its genotype and the environment.

(2) The expression of a particular trait, for example, skin color, height, behavior, etc., according to the individual’s genetic makeup and environment.

A genotype is the genetic programming defined by an organism’s DNA, but phenotype is the physical manifestation of that programming as influenced by environment. If it still sounds esoteric, let’s use some examples from my three year-old. No, he’s not an expert. These aren’t examples that he came up with (we’re still working on colors and counting). He is the example. I realize this will be deviating from my primary photosynthetic focus, but I’ve spent a lot of time observing him over the last few years and I have a complete dataset on him.

At a basic level, most adjectives describing my son are all ways of describing of his phenotypes. He is a boy. He has blue eyes and brown hair. All of these characteristics are determined by his genotype. These are simple things that are always true of him no matter what his environment is.

When talking about phenotypes, it is sometimes useful to speak of continuous variation of a phenotype. This is relevant when discussing a population of the same organism. While members of a population may have similar phenotypes, they are not identical. Here again, three year-olds can vary significantly. Their developmental range for things like learning letters, numbers and colors can be quite different, but this is still a normal range of continuous variation. So, the fact that my son has the layout of our local zoo memorized and can tell you all of the animals in it, but still guesses ‘red’ every time you ask him what color something is*, gives him a distinct place within the continuous variation of knowledge for a normal human three year-old.

A mutant phenotype is a specific variant that is significantly different from the normal range of variation. Usually mutant phenotypes yield a defect in the organism. In my son’s case, he is a loveofpeanutbuttermutant**. In the case of my husband and I (his biological parents), we are LOVEOFPEANUTBUTTER+ normal. In genetics usage, lowercase italics indicate a mutant or defective copy of a gene or a mutant version of a phenotype; uppercase non-italics indicate the standard, normal (aka wild-type) version of a gene or phenotype. So you should understand from my previous statement that both my husband and I love peanut butter (so much that we lack the self-control to even keep it in our house, seriously the jar would be completely empty after only two nights). Our son, on the other hand, has maybe eaten three bites of any kind of PB&J sandwich in his entire life. I know my son’s genotype should make him LOVEOFPEANUTBUTTER+ (because he gets a version of this trait from both of his parents), but his apparent phenotype is loveofpeanutbutter. My only explanation for this pattern of inheritance is that he acquired a mutation in this critical gene or trait at some point giving him this mutant phenotype. No, I do not accept that loveofpeanutbutter is part of a normal continuous variation for humans; it would shake my worldview to its core.

Another specific category of phenotype is the variegated phenotype. In a variegated mutant, random parts of an organism show a mutant phenotype while other parts appear normal. In the case of my three year-old, his variegation is conditional (more on that below). Upon serving him juice instead of milk (or vice versa depending on the time of day and other factors I have not determined), his skin changes to different colors as a result of this egregious injustice. His face turns mostly red with a couple of distinct white spots on his forehead near his eyebrows. This splotchy coloring is an excellent analogy for a variegated phenotype (typically variegation is a permanent state for a given individual). In my son’s case, this is not necessarily a mutant phenotype; he gets that one honest from me.

Other phenotypes are conditional, meaning they have a significant influence from the environment. My son’s bed-time routine has a conditional phenotype. If it is before 8:30pm, he is relatively easily convinced to brush his teeth, have a bath and put on PJs for bed. If it is after 8:30pm, he cries (not quite variegated), starts to speak in a pitch that hurts the dogs’ ears and resists every step of our normal routine. His internal clock is very finely tuned for this response and this has been experimentally verified on numerous occasions.

The last phenotype is a special type of conditional phenotype dependent on temperature. The temperature-sensitive phenotype is a special type of mutant phenotype that is extremely useful to scientists. Under certain permissive temperatures, the organism has a normal phenotype. Under restrictive or non-permissive temperatures (usually higher), the organism has a mutant phenotype. It is often useful for scientists to switch an organism’s phenotype from normal to mutant in the lab by a simple condition change for experimental purposes. Our three year-old has a dreadful temperature-sensitive phenotype. If the thermostat in our home is 72 ± 1 oF at bed time, he will sleep peacefully through the night in his own bed. If the thermostat is above 75 oF at bed time, he will not go to sleep right away; numerous requests will be made for toys, books, water etc. before he goes to sleep. Then he sleeps for thirty minutes longer than his parents’ bed time whereupon he climbs in bed with them and proceeds to flop, kick, jab, toss and turn for four to six hours until one to two hours before the alarm goes off in the morning when he sleeps peacefully. I have not found this particular temperature-sensitive phenotype useful for any purpose as a parent or scientist.

Yes, these examples are all a bit silly, but they get the point across without resorting to more unrelate-able jargon. For extra credit, can you think of your own examples using your family, friends, co-workers, or pets?


*Don’t be alarmed. I do think he sees color because he sorts his crayons, cars etc. according to color and he can do the Melissa and Doug puzzles matching same-size, but different-colored pieces appropriately. I just think he doesn’t want to tell me or anyone what color anything is. We’re watching it.

**Geneticists get to come up with creative names for new mutants and their underlying genes based on their phenotypes. I am a biochemist, so I never get this opportunity except here on my blog.


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