user3347: This is in regards to the following question: Are there known examples where an evolved mechanism "echoes" one originally provided by the environment?, although it also speaks to a much broader point regarding the site's scope.
The question linked above is quite a difficult one to ask, because I'm a professional in quite a specialised field, and I'm hoping to obtain answers from other professionals, about something that's really very specific. (I would say it's much more specific than the vast majority of questions on this site.) However, despite my attempts to make the question comprehensible to a broader audience than the one it's really intended for, a selection of users in the comments and answers failed to understand it, interpreting it instead as something very simple, along the lines of "please give me examples of something that's evolved."
Some users understood the question perfectly well, but some didn't, and as a consequence of this misunderstanding the question has been closed as "too broad". I've wracked my brain trying to think of some way to avoid the misunderstanding that caused this, but I really have no idea how to do it. I think someone with the knowledge required to answer the question will not have any problem understanding it, but I don't know how to simultaneously make it more comprehensible to a lay audience, so that it will be allowed to remain open.
Moreover, it seems a bit problematic that I should have to do this at all. My experiences here have generally been unwelcoming, with three out of four of my questions accumulating close votes from the same small set of users, who in each case either had trouble understanding the question, or misinterpreted it as asking for something much broader than it actually was. I repeat that I'm a professional scientist with many papers to my name (though crucially I'm not a biologist, which I guess might be the core of the problem), and I know that these questions will be easily comprehensible to someone who can answer them. It's right that questions should be closed if they're badly posed, but on this site I get the distinct impression that questions can be unwelcome merely because they're difficult. It will be hard to attract professionals to your site if others have similar experiences.
In any case, my questions are (1) what, if anything, can I do to have this particular question re-opened, and (2) is it worth having a broader discussion about the questions you would like to accept that might come from, or be aimed at, a specialised audience; or which might come from professionals (like me) in other fields?

user5198: Perhaps I'm not the right person to answer this, as I've only been involved here for a short few months, but I do have some observations.
I think this site is quite open to professionals. I am a practicing physician who also has a PhD in Molecular Biology. As such, I can recognize a good question in a number of fields in Biology, and when I see good (or funny or interesting or sincere) ones (in my areas of expertise), I'm happy to answer to the best of my ability. When I recognize an off-topic one, I do vote to close (after I familiarize myself with the site's expectations).
However, "Biology" is a very wide topic, and I would guess even a few dozen professionals with great expertise in their different fields can be on this site and only have a superficial understanding of the fields of the others. That's certainly my perspective: I can understand some of WYSIWYG's field, but not a lot. I would guess (but not presume) that I know a lot more anatomy & physiology than he does. 
I read and reread your question. Basically I understand it, but I cannot for the life of me give you an example of something even you don't believe exists, much less with a good bibliographic reference to support [your] claim that there aren't any. Nor can I prove you wrong with a good example instead. 
I hope I wasn't one of your closers, but I may well have been. You're asking someone to cover a very broad area of evolutionary biology here. A narrow question is a much better fit with the SE model, and much more likely to garner a good response. 
I don't mean this to sound unkind (the written word in my hands is rather, but not intentionally, cold) but if you are a specialist in some field, you must know how to do scholarly searches to answer your own questions, or to narrow your question. If you're not a biologist but a specialist on the origins of life, what is, may I ask, your specialty? I really can't guess. (I did read your profile.)
A concluding observation (maybe two). Trying to pin down an answer in comments is not a good approach to dealing with a broad or unclear question. This comment after WYSIWYG's answer to one of your questions is an example of why this doesn't work:

The linked article appears to be referring to organelles within eucaryotic cells, rather than to the cell as a whole. I'm specifically interested in whether there are any cells that entirely lack ATP synthase, not just in the organelles, but in the outer membrane as well. 

Before I made a comment like that, I would have searched "do eukaryotic cell membranes have ATP synthase" and had a head start on the answer.
The best way to get a feeling for an SE site is to participate in it. To ask an occasional question and then make an somewhat accusatory meta post/comment chain will not work to your advantage.
Again, I'm a relative newcomer here, so I do not speak for the site, just myself.

user3340: Are professionals welcome here?
Of course they are. We need more of them.


I repeat that I'm a professional scientist with many papers to my name
  (though crucially I'm not a biologist, which I guess might be the core
  of the problem), and I know that these questions will be easily
  comprehensible to someone who can answer them.

Many of us are professional scientists or at least doing research in different aspects of biology. Are you really clear with what you want to ask; Have you given some thought about it yourself? If the answer is "yes" then perhaps you are not asking it exactly. I would want to add that your question is too long and the precise crux of the question seems to be lost. This is my opinion; you can call me a layman for it. 


To help me assess how realistic this kind of hypothesis is, I'm
  looking for examples of the same kind of thing occurring in modern
  biology.

What is modern biology. Do you mean biological occurrences from modern era (after the evolution of terrestrial plants and animals, perhaps??). Or do you mean is it possible to create a new function using the modern tools of biology?
You say that gene transfers are not what you are interested in but you rather want to know if a function was created de-novo. 
When user137 gave an example of temperature regulation, you say you want something more complex. You should really define complex. You reiterate the Krebs cycle and ion-gradient example and simply add that you are looking for metabolic processes like that. You have to understand that these processes took ages to evolve and any living system builds on what it already has. It then simply follows that all metabolic pathways, drug resistance genes etc have been invented by the cell by improvising the available set of genes. 
Are you saying that you want something like the evolution of molecular motors: abiotic to biotic (and anything else would not qualify as an answer)?

You keep commenting that "this is my fault for not being clear enough", but you make no attempt to edit and clarify the question. Instead, you blame others for being ignorant and closing your question just because they cannot answer it. This is no professional behavior- saying something in the comments and saying something else here. 

Anyways I am not holding any grudges. And for your questions:

In any case, my questions are (1) what, if anything, can I do to have
  this particular question re-opened, and (2) is it worth having a
  broader discussion about the questions you would like to accept that
  might come from, or be aimed at, a specialised audience; or which
  might come from professionals (like me) in other fields?


[Even though it is reopned this is my opinion on what should be done] If it is closed as broad, then narrow the question down to a precise issue. Examples that you cite should clarify the question or provide analogy in some way. Also make the question (if possible) a little short; Too long a post is difficult to read.
IMO questions are welcome from all kinds of people interested in biology, however, SE is not designed for discussions. If you have a broad topic consisting of many questions then ask them separately. 


user6: I've reopened it for now. The issue seems to me that this kind of question asking for a list of examples is close to the kind of list questions that generally don't work well on SE sites. 
I would prefer such questions to be phrased more conceptual, and not just asking for examples. It is always a good idea to ask in a way that encourages more elaborate answers, but it is not a necessity.

3347: <p>This is in regards to the following question: <a href="https://biology.stackexchange.com/questions/26274/examples-where-a-species-has-evolved-a-function-that-was-originally-provided-by">Are there known examples where an evolved mechanism &quot;echoes&quot; one originally provided by the environment?</a>, although it also speaks to a much broader point regarding the site's scope.</p>

<p>The question linked above is quite a difficult one to ask, because I'm a professional in quite a specialised field, and I'm hoping to obtain answers from other professionals, about something that's really very specific. (I would say it's much more specific than the vast majority of questions on this site.) However, despite my attempts to make the question comprehensible to a broader audience than the one it's really intended for, a selection of users in the comments and answers failed to understand it, interpreting it instead as something very simple, along the lines of "please give me examples of something that's evolved."</p>

<p>Some users understood the question perfectly well, but some didn't, and as a consequence of this misunderstanding the question has been closed as "too broad". I've wracked my brain trying to think of some way to avoid the misunderstanding that caused this, but I really have no idea how to do it. I think someone with the knowledge required to answer the question will not have any problem understanding it, but I don't know how to simultaneously make it more comprehensible to a lay audience, so that it will be allowed to remain open.</p>

<p>Moreover, it seems a bit problematic that I should have to do this at all. My experiences here have generally been unwelcoming, with three out of four of my questions accumulating close votes from the same small set of users, who in each case either had trouble understanding the question, or misinterpreted it as asking for something much broader than it actually was. I repeat that I'm a professional scientist with many papers to my name (though crucially I'm not a biologist, which I guess might be the core of the problem), and I <em>know</em> that these questions will be easily comprehensible to someone who can answer them. It's right that questions should be closed if they're badly posed, but on this site I get the distinct impression that questions can be unwelcome merely because they're <em>difficult</em>. It will be hard to attract professionals to your site if others have similar experiences.</p>

<p>In any case, my questions are (1) what, if anything, can I do to have this particular question re-opened, and (2) is it worth having a broader discussion about the questions you would like to accept that might come from, or be aimed at, a specialised audience; or which might come from professionals (like me) in other fields?</p>
 5198: <p>Perhaps I'm not the right person to answer this, as I've only been involved here for a short few months, but I do have some observations.</p>

<p>I think this site is quite open to professionals. I am a practicing physician who also has a PhD in Molecular Biology. As such, I can recognize a good question in a number of fields in Biology, and when I see good (or funny or interesting or sincere) ones (in my areas of expertise), I'm happy to answer to the best of my ability. When I recognize an off-topic one, I do vote to close (after I familiarize myself with the site's expectations).</p>

<p>However, "Biology" is a very wide topic, and I would guess even a few dozen professionals with great expertise in their different fields can be on this site and only have a superficial understanding of the fields of the others. That's certainly my perspective: I can understand some of WYSIWYG's field, but not a lot. I would guess (but not presume) that I know a lot more anatomy &amp; physiology than he does. </p>

<p>I read and reread your question. Basically I understand it, but I cannot for the life of me give you an example of something even you don't believe exists, much less with <em>a good bibliographic reference to support [your] claim that there aren't any</em>. Nor can I prove you <em>wrong with a good example instead</em>. </p>

<p>I hope I wasn't one of your closers, but I may well have been. You're asking someone to cover a very broad area of evolutionary biology here. A narrow question is a much better fit with the SE model, and much more likely to garner a good response. </p>

<p>I don't mean this to sound unkind (the written word in my hands is rather, but not intentionally, cold) but if you are a specialist in some field, you must know how to do scholarly searches to answer your own questions, or to narrow your question. If you're not a biologist but a specialist on the origins of life, what is, may I ask, your specialty? I really can't guess. (I did read your profile.)</p>

<p>A concluding observation (maybe two). Trying to pin down an answer in <em>comments</em> is not a good approach to dealing with a broad or unclear question. This comment after WYSIWYG's answer to one of your questions is an example of why this doesn't work:</p>

<blockquote>
  <p>The linked article appears to be referring to organelles within eucaryotic cells, rather than to the cell as a whole. I'm specifically interested in whether there are any cells that entirely lack ATP synthase, not just in the organelles, but in the outer membrane as well. </p>
</blockquote>

<p>Before I made a comment like that, I would have searched "do eukaryotic cell membranes have ATP synthase" and had a head start on the answer.</p>

<p>The best way to get a feeling for an SE site is to participate in it. To ask an occasional question and then make an somewhat accusatory meta post/comment chain will not work to your advantage.</p>

<p>Again, I'm a relative newcomer here, so I do not speak for the site, just myself.</p>
 3340: <p><strong>Are professionals welcome here?</strong></p>

<p>Of course they are. We need more of them.</p>

<hr>

<blockquote>
  <p>I repeat that I'm a professional scientist with many papers to my name
  (though crucially I'm not a biologist, which I guess might be the core
  of the problem), and I know that these questions will be easily
  comprehensible to someone who can answer them.</p>
</blockquote>

<p>Many of us are professional scientists or at least doing research in different aspects of biology. Are you really clear with what you want to ask; Have you given some thought about it yourself? If the answer is "yes" then perhaps you are not asking it exactly. I would want to add that your question is too long and the precise crux of the question seems to be lost. This is my opinion; you can call me a layman for it. </p>

<hr>

<blockquote>
  <p>To help me assess how realistic this kind of hypothesis is, I'm
  looking for examples of the same kind of thing occurring in modern
  biology.</p>
</blockquote>

<p>What is modern biology. Do you mean biological occurrences from modern era (after the evolution of terrestrial plants and animals, perhaps??). Or do you mean is it possible to create a new function using the modern tools of biology?</p>

<p>You say that gene transfers are not what you are interested in but you rather want to know if a function was created <em>de-novo</em>. </p>

<p>When user137 gave an example of temperature regulation, you say you want something more complex. You should really define <strong>complex</strong>. You reiterate the Krebs cycle and ion-gradient example and simply add that you are looking for metabolic processes like that. You have to understand that these processes took ages to evolve and any living system builds on what it already has. It then simply follows that all metabolic pathways, drug resistance genes etc have been invented by the cell by improvising the available set of genes. </p>

<p>Are you saying that you want something like the evolution of molecular motors: abiotic to biotic (and anything else would not qualify as an answer)?</p>

<hr>

<p>You keep commenting that "<em>this is my fault for not being clear enough</em>", but you make no attempt to edit and clarify the question. Instead, you blame others for being ignorant and closing your question just because they cannot answer it. This is no professional behavior- saying something in the comments and saying something else here. </p>

<hr>

<p>Anyways I am not holding any grudges. And for your questions:</p>

<blockquote>
  <p>In any case, my questions are (1) what, if anything, can I do to have
  this particular question re-opened, and (2) is it worth having a
  broader discussion about the questions you would like to accept that
  might come from, or be aimed at, a specialised audience; or which
  might come from professionals (like me) in other fields?</p>
</blockquote>

<ol>
<li>[<em>Even though it is reopned this is my opinion on what should be don</em>e] If it is closed as broad, then narrow the question down to a precise issue. Examples that you cite should clarify the question or provide analogy in some way. Also make the question (if possible) a little short; Too long a post is difficult to read.</li>
<li>IMO questions are welcome from all kinds of people interested in biology, however, SE is not designed for discussions. If you have a broad topic consisting of many questions then ask them separately. </li>
</ol>
 6: <p>I've reopened it for now. The issue seems to me that this kind of question asking for a list of examples is close to the kind of list questions that generally don't work well on SE sites. </p>

<p>I would prefer such questions to be phrased more conceptual, and not just asking for examples. It is always a good idea to ask in a way that encourages more elaborate answers, but it is not a necessity.</p>
