Learn English – Comma use: “from the ground up” or “from the ground, up”

Ordinarily parenthesis should be marked with commas on both sides. But Fowler recommends that the first comma should be left out after a coordinating conjunction if what follows is a simple adverbial phrase—if I interpret him correctly. (Coordinating conjunctions are and, or, but, and possibly some semi-conjunctive adverbs like so, therefore, however, etc.) The comma should be retained before a subordinate clause or when its omission would cause ambiguity. This probably includes conjunctions that are not at the beginning of a sentence. Fowler's advice seems balanced and practical.

• Cleopatra appeared poised and composed. But on the inside, she was seething with rage. — Simple adverbial phrase at the beginning of a sentence.

• Her only option was to support Mark Anthony once again. But, if he should perish, it would be the end of her. — Not a simple adverbial phrase but a clause.

• She knew her cause was lost and, in a fit of final despair, had a serpent brought in to extinguish her life with its venom. — Not at the beginning of a sentence.

The relevant text from Fowler's The King's English follows. He is arguing for general laxity with adverbial phrases, and would generally allow both commas and no commas around them. He goes on to say that, if commas are used, one must never omit one but write the other; however, he gives the above rule as an exception, in order to avoid an abundance of commas, logical though they might be.

Laxity once introduced, however, has to be carefully kept within bounds. It may be first laid down absolutely that when an adverbial clause is to be stopped, but incompletely stopped, the omitted stop must always be the one at the beginning, and never the one at the end. Transgression of this is quite intolerable; we shall give several instances at the end of the section to impress the fact. But it is also true that even the omission of the beginning comma looks more and more slovenly the further we get from the type of our above cited sentence. The quotations immediately following are arranged from the less to the more slovenly.

• His health gave way, and at the age of fifty-six, he died prematurely in harness at Quetta.—Times.

• If mankind was in the condition of believing nothing, and without a bias in any particular direction, was merely on the look-out for some legitimate creed, it would not, I conceive, be possible...—Balfour.

• The party then, consisted of a man and his wife, of his mother-in-law and his sister.—F. M. Crawford.

• These men in their honorary capacity, already have sufficient work to perform.—Guernsey Evening Press.

It will be observed that in the sentence from Mr. Balfour the chief objection to omitting the comma between and and without is that we are taken off on a false scent, it being natural at first to suppose that we are to supply was again; this can only happen when we are in the middle of a sentence, and not at the beginning as in the pattern Cranmer sentence.

I don't believe you can insert a gapping comma there for two reasons.

1. Because it puts and wiring into parenthesis.

   That is, your second example can be read as

   Memory can be implemented by delays by various walls to guide the one extra bit per site needed to represent the walls.

   I don't think that's right.

2. Because the first comma could be read as a sort of Oxford comma:

   Memory can be implemented by delays and wiring, by various walls to guide the one extra bit per site needed to represent the walls.

   That doesn't look right either.

Not every omission needs a gapping comma, and there are some instances as here where adding one is a hindrance to understanding.