TABLE 3.

Code definitions for knowledge-network features

Coding Dimension	Code	Definition	Example Quote
Nature of Connections	Mechanistic	Includes many entities and activities that explain how interactions across levels of organization cause the phenomenon.	“If the cell is in the context of some sort of environment, it upregulates a particular gene and that gene is maybe a secretory protein, or a hormone, or something along those lines that get secreted from the cell so that another cell can respond and knows what's going on.” – Instructor one*
	Specified Causal	Names at least one player that is a causal factor. Connection often lacks activities.	“…the pattern of genes that is expressed can be responses to changes in environment such as signals from other cells.” – Student three
	Unspecified Causal	Notes that one subsystem leads to another subsystem, but provides no details to explain how this occurs. This causation is general and may be part of a temporal sequence.	“…gene regulation directly affects phenotype…” – Student two
	Associative	A relationship is based purely on superficial features or ideas without any causal reasoning. Participant states an attribute or property without a causal link or without causal justification	“…your phenotype and your behavior is your cell–cell communication…” – Student seven
Level of Organization of Players	Undefined	1) Vague or unknown player (e.g., “stuff”, “something”, and “you”)OR2) A player with potentially variable level of organization that is not specified (usually abstract) such as “phenotype”	“…the genotype controls…cell–cell communication. But… on a bigger scale…” – Student two
	Environmental	The surrounding environment of a single-celled organism, a cell within a multicellular organism, or a multicellular organism	“…the pattern of genes that is expressed can be a response to changes in the environment…” – Student three
	Organismal	A multicellular, higher-level organism	“…your proteins that you make and [how] they're utilized in your body…are gonna display different phenotypes…” – Student seven
	Cellular	A single cell or more than one cell (group of cells)	“…the cells obviously have to be able to communicate with each other…” – Student four
	Macromolecular	A large macromolecule, typically composed of smaller subunits such as proteins, DNA/ RNA, and carbohydrates	“…proteins are created in response…” – Student one
	Molecular	1) A small, molecule such as ligands or may be building block molecules that form a macromolecule (e.g., amino acids and nucleotides)OR2) Describes chemical or atomic interactions such as chemical bonds	“So the primer that's sitting on the DNA strand, for example, that will start the nucleotide sequence.” – Student six
Localization of Processes	Unspecified	1) Vague, uncertain, or ill-defined statements of where the process is occurring; two processes are linked without any detailed information or specific steps such as “cells lose flagella through gene regulation”OR2) For instances where the players involved in the process could be located at different localizations and there are no contextual clues to indicate where such as “signaling occurs”	“…the cells all form together then to make a gene which is like a larger scale…” – Student three
	Outside a Cell	Anywhere exterior of the cell not involving the plasma membrane (e.g., extracellular fluid and environment)	“…the cells need to communicate… like in response to what the cell is like going through in its environment…” – Student five
	At the Membrane/ Spanning	1) Interactions happening at the cell surface (e.g., cell–cell, molecule to receptor, and membrane to surface)OR2) Processes occurring across the cell membrane such as exocytosis	“…that signaling molecule is released from the cell and binds to the receptor of another cell…” – Instructor six*
	Inside a Cell	Anywhere interior of the cell (e.g., cytoplasm)	“…it could be cell–cell communication, if it goes to the nucleus where gene expression is regulated…” – Student one

*Instructor quotes included to illustrate the code, because there were no student quotes.