user389: This is a certainly a real problem for biologists. One reads a paper but they aren't sure how to fully understand or interpret a paper or a series of papers. Good question along these lines would be: Does GFAJ-1 use Adenosine triarsenate as its energy currency?
How are the various classes of E coli genes determined?
Would it be appropriate to ask further questions along these lines? What if they involved certain methods? Because I have plenty of questions.

user307: I personally think that both of those questions (and those type of questions) are informative, interesting and most importantly well received by the community (judging by their upvotes). Even the fact that you're inherently referencing an article with this type of question may be a plus. I can't see why they wouldn't be appropriate :).
EDIT: As @Armatus points out, there is at least one exception. I don't think the community would tolerate  or benefit from a "What are your impressions about this article?" or a "I don't understand this article: explain it".

389: <p>This is a certainly a real problem for biologists. One reads a paper but they aren't sure how to fully understand or interpret a paper or a series of papers. Good question along these lines would be: <a href="https://biology.stackexchange.com/questions/1648/does-gfaj-1-use-adenosine-triarsenate-as-its-energy-currency">Does GFAJ-1 use Adenosine triarsenate as its energy currency?</a></p>

<p><a href="https://biology.stackexchange.com/questions/1758/how-are-the-various-classes-of-e-coli-genes-determined">How are the various classes of E coli genes determined?</a></p>

<p>Would it be appropriate to ask further questions along these lines? What if they involved certain methods? Because I have plenty of questions.</p>
 307: <p>I personally think that both of those questions (and those type of questions) are informative, interesting and most importantly well received by the community (judging by their upvotes). Even the fact that you're inherently <a href="https://biology.meta.stackexchange.com/questions/294/should-we-always-ask-for-references">referencing an article</a> with this type of question may be a plus. I can't see why they wouldn't be appropriate :).</p>

<p><strong>EDIT:</strong> As @Armatus points out, there is at least one exception. I don't think the community would tolerate  or benefit from a <em>"What are your impressions about this article?"</em> or a <em>"I don't understand this article: explain it"</em>.</p>
