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What is the meaning of the word canonical in a scientific context? This is an example that I do not understand:

BDNF is a member of the neurotrophin family of growth factors, which are related to the canonical nerve growth factor.

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Short Answer

The word canonical in this context implies that nerve growth factor is the original, standard or prototype of some sort (in relation to a class of biological agents).

Without knowing details of growth factors I found the sentence slightly ambiguous. As I suspected, it means that NGF is either the original growth factor or the original representative of the “neurotrophin family of growth factors”, which includes BDNF (brain-derived growth factor) — see Wikipedia article. However the use of the word “related” could be interpreted incorrectly to mean that the neurotrophins are in a different family from NGF.

Relationship to the general meaning of the word in English

The excellent Oxford Dictionary, accessible from any iPhone, has this as the first meaning of the word canon:

  1. A general law, rule, principle or criterion by which something is judged.

The appointment violated the canons of fair play and equal opportunity

So its ecclesiastical connotation (in church law) is only one example of the application of the word, and is not intrinsic to it. The word comes from Middle English through Latin from the Greek, kanōn, meaning rule. Hence it has been applied in many spheres to things that are rules or standards.

Another examples of ‘canonical’ in biological science

Perhaps the most well-known usage is in relation to the base-pairing of nucleic acids. A definition by implication can be found in the Wikipedia entry for ‘Non-canonical base pairing’

The standard Watson-Crick base pairs (which are adenine–thymine in DNA, adenine–uracil in RNA, and guanine–cytosine in both DNA and RNA).

(The non-canonical base-pairs are those that are found outside the context of double-helical DNA–DNA or DNA-RNA duplexes, for example G–U base-pairs in dsRNA, wobble base-pairing between mRNA and tRNA, and other base-pairs in non-duplex components of RNA structure.)

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Though David's answer is technically correct, I offer an alternative for those who struggle with the term in broader contexts.

Definition

Canonical simply means relating to a historically established paradigm, or relating to a common or standard model (which simplifies things!). For example, a biochemical pathway or a mechanism, for example, may be understood to include certain typical players or long-understood elements or interactions. These are canonical elements. They relate to the scientific canon. They depend on the history of discovery and organization of our theories, rather than any biological phenomenon.

Example

For instance, a synapse is canonically composed of a pre-synaptic neuron and a post-synaptic neuron. This has been long known and to this day scientists broadly speak in terms of the two, as a simplification of the system. However, most synapses are tripartite, including a glial cell cradling and modulating the environment between the communicating neurons. The glial cell can be considered to be the non-canonical element, even though it may be essential, or very important in the system. But it hasn't been studied as long, and introduces more considerations and complexities to think about which go beyond a simple way of thinking about it.

The use of the word

Some pathways or mechanisms have been strictly defined and outlined, where one can clearly draw the line between the canonical and non-canonical elements. There is no flexibility in how you use the word. On the other hand, other times the word is used in cases of systems where there is no strict definition dividing the two, it's just a judgment call, of what most scientists consider central, primary and emblematic (as opposed to peripheral, or secondary, or not validated enough 'to have entered the canon') to the system. There the use of the term canonical is colloquial!

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