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Varous definitions of the word "transparent" seem almost contradictory:

  1. nearly invisible
  2. easy to perceive
  3. functioning without the user's perception

The first two definitions seem to be in tension. A material is "transparent" if one can clearly perceive the detail of whatever else is underneath it (meaning the object itself is hardly detected and difficult to perceive). But (in a figurative or abstract sense) "transparent" can also mean that the object is easy to detect and amenable to inspection. "Transparent" might be applied to a business practice that is void of any deceptiveness, or to a motive that is rife with deceptiveness.

In computing, we often say a detail is "transparent" when we mean it is encapsulated. That is, the handling of the detail is invisible or implicit rather than being exposed and made explicit. (A modular design philosophy is that most internal details should be shielded from outside view, to simplify how components can interact. But in other contexts, transparency is the opposite of shielding things from view.)

How did these differing meanings come to be? To avoid ambiguity (particularly in the computing context) would any other terms be clearer?

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    It's a contranym. Certain usages are antonymic. Transparent mediums are impossible to discern; transparent attempts to buy votes are easily perceived. If the meanings weren't etymologically connected, there'd be two homographs. A typical example from the internet: '... hard to see it unless you look closely because it's transparent.' Yes, the connection is that with a transparent medium, it's easy to see beyond, while with a transparent campaign, it's easy to see through. But the end-definitions mentioned are contrary.
    – Edwin Ashworth
    Commented Dec 30, 2023 at 18:53

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Various definitions of the word "transparent" seem almost contradictory:

  1. nearly invisible

  2. easy to perceive

  3. functioning without the user's perception

Your question is flawed as you do not give the source of, and context for, the proposed definition. [If you have invented them yourself, then it would appear that you have cherry-picked them.]

Transparent has a base meaning that associated with both "unimpeded / clear transmission" and "light".

OED

1.a. Having the property of transmitting light, so as to render bodies lying beyond completely visible; that can be seen through;

1813 Uncrystallized quartz is seldom transparent, most frequently translucent, but sometimes opaque. R. Bakewell, Introduction to Geology i. 34

Like many English words it has extended and figurative senses in which "light" is not necessarily the primary element or is not emphasised and "unimpeded / clear transmission [of something]" is an emphasised element and vice versa.

The answer to your question is therefore "No. It has meanings that are linked by its primary definition."

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  • It's a contranym. Transparent mediums are impossible to discern; transparent attempts to buy votes are easily perceived. If the meanings weren't etymologically connected, there'd be two homographs. A typical example from the internet: '... hard to see it unless you look closely because it's transparent.' Yes, the connection is that with a transparent medium, it's easy to see beyond, while with a transparent campaign, it's easy to see through. But the end-definitions mentioned are contrary.
    – Edwin Ashworth
    Commented Dec 30, 2023 at 18:50
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    @EdwinAshworth Transparent does not mean “invisible” or “unable to be perceived.” Transparent mediums can be seen through; transparent attempts to buy votes can be seen through.
    – Greybeard
    Commented Dec 30, 2023 at 22:58
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The word has these two opposite metaphorical meanings, that are both based on the same literal meaning, because the metaphors they embody work differently. (I speak here of two meanings, because 3 in the question is a special case of 1.) The software engineers’ use of the term takes the inner workings of the software to be themselves, metaphorically speaking, transparent, and thus invisible to the user: the user sees through them whatever is intended to be in the user's experience, as one would see something through a literally transparent medium.

In other contexts the implied metaphor is that of box, or an envelope that is transparent, so that what is inside it is visible. When we say, for example, that the deliberations of a political body are transparent, we mean that there are no obstacles to our observing them clearly; when we complain that they are not transparent, we mean that something has been put in place that hides them from our scrutiny.

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When it comes to computer-based tasks, you're not 'shielding things from view' you're opening up the part the user needs to see and work on, without hinderance from confusing complexity which may mask the simplicity of the user experience.

Your machinations are transparent, leaving the user's experience in clear view.

A background process operates transparently. The user cannot see it, nor do they need to; it can operate without their intervention or even knowledge as to what is happening in the background.

Take something 'simple' like a browser. The user clicks a link or a bookmark, the web site is shown to them.
Done.
They have no need or desire to be caught up in the complexity of that 'simple' process. Most users have little concept of DHCP, DNS, transport layers, even the difference between http & https.
They just don't need to know all that to see what TikTok or Instagram is presenting for today's delight and delectation.

The process is transparent.

From a business perspective, transparency is 'open to inspection' without hinderance. 'A motive that is rife with deceptiveness' is the opposite of transparent; you would be looking toward opacity rather than transparency.

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