Cryptic crossword clue
Natural identifier of two pens: the first one has run out 9

The most common and most likely answer to this crossword clue is the 9 letter word BIOMARKER

I've seen this crossword clue in The Guardian
B
I
O
M
A
R
K
E
R

Buddy explains!

The straight part
We know that "Natural identifier" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case natural identifier = biomarker.
The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.
This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.

Crossword Answer definitions

BIOMARKER noun
  1. A substance used as an indicator of a biological state, most commonly disease.

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