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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?

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    $\begingroup$ A lot of seemingly valid questions are closed. Sometimes it's a clear misunderstanding of the question by the closers. Sometimes questions where the answer is no (perhaps obviously) are closed instead of answered. This site has somewhat of an identity crisis where different people have different ideas of what they want to the site to be. $\endgroup$ – canadianer Jan 1 '15 at 19:22
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    $\begingroup$ Yes, very welcome! In this case the problem is/was probably to phrase it in appropriate terms and to remove some ambiguity. $\endgroup$ – fileunderwater Jan 1 '15 at 20:14
  • $\begingroup$ @fileunderwater could you give me some specific hints about what terms would be appropriate, and what you find ambiguous about it? Since I'm an expert in a different field, part of the reason for the question is that I don't know the appropriate terms, so if you have a good idea what the appropriate terms are then I would be extremely grateful if you would post it - an outline of the terminology used to describe this particular concept would make an excellent answer to my original question. $\endgroup$ – Nathaniel Jan 2 '15 at 1:14
  • $\begingroup$ @Nathaniel I've added an answer/comment directly to your question instead. $\endgroup$ – fileunderwater Jan 4 '15 at 23:05
  • $\begingroup$ Yes.‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍ $\endgroup$ – J. Musser Jan 6 '15 at 2:49
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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.

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    $\begingroup$ I appreciate your concerns about my question (although I'm unsure of how to interpret the "more conceptual" comment). If those were the concerns of the close voters, they would have been easy to address: the question is not asking for a list of examples but for a single example, of something that may or may not ever have happened, and more than that it's asking for terminology and pointers into the literature; it would have been simple to edit to emphasise those things if this were the issue. (...) $\endgroup$ – Nathaniel Jan 2 '15 at 0:51
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    $\begingroup$ (...) but if you read the comments you'll see that the reasons for the close votes don't at all resemble your very reasonable points. Rather, the issue seems to be a kind of anti-intellectualism on the part of the close voters. I'm asking for something that's inherently difficult for them to understand, and instead of asking for clarification they're demanding that I ask something simpler. The attitude seems to be that if a question is not easily and instantly comprehensible to the user(s) in question with their particular background then it should be closed (...) $\endgroup$ – Nathaniel Jan 2 '15 at 0:58
  • $\begingroup$ (...) regardless of whether this is because it's badly written or just because it's outside their field. Now, this is your site, and it's up to you whether to just accept this or do something about it, but if it were me I would consider this an abuse of the voting system, and I would contact the users involved and let them know their accounts will be suspended for increasing amounts of time unless they play by the rules. $\endgroup$ – Nathaniel Jan 2 '15 at 1:01
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    $\begingroup$ @Nathaniel I removed your last comment, these discussions tend to go a lot better if they are focused on specific behaviour and issues instead of specific persons. So I'd like to keep this about the general issue without naming individual users. I also wouldn't attribute these closings to any kind of anti-intellectualism, but an effort to deal with some low quality questions we received. The big problem is probably that we don't all agree yet on what kind of questions we want here. $\endgroup$ – Mad Scientist Jan 2 '15 at 9:25
  • $\begingroup$ Fair enough, I expected you to delete it. If there's a disagreement about which questions should be allowed then I strongly believe in the Stack Exchange tradition of discussing and voting on it on meta, rather than allowing people to use close votes however they wish. The problem is that currently it's just a lottery whether a question will be allowed or not. If the community doesn't want questions of a certain type then it should reach a consensus and form a specific policy, so that people can know that they're not supposed to ask them. $\endgroup$ – Nathaniel Jan 3 '15 at 14:45
  • $\begingroup$ If you don't do that it's bad for everyone. People will keep putting effort into asking questions that you consider bad, and you (the community) will keep having to close them. Admittedly not everyone always reads the rules, but some people do, so in the long run it will save you quite a lot of work. $\endgroup$ – Nathaniel Jan 3 '15 at 14:48
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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?

  1. [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.
  2. 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.
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  • $\begingroup$ Thank you for your comments. They are helpful. $\endgroup$ – Nathaniel Jan 3 '15 at 14:22
  • $\begingroup$ I think the length issue might be the main one here. If I were intimately familiar with the terminology used to describe this subject (if indeed there is any), then I daresay I could express the question concisely. I would also have less need to ask it of course. But since I'm not, I have little choice but to try and spell out in detail what I mean. I did my best to do that, but I still wasn't understood by all readers, and in fact I made it longer in response to your initial comments in an attempt to clarify it. $\endgroup$ – Nathaniel Jan 3 '15 at 14:22
  • $\begingroup$ As an example: you ask what I mean by "modern biology". This is a standard term in origins of life, but perhaps I shouldn't have used it without explanation. It refers to all biology that came after LUCA (i.e. prokaryotes, eukaryotes and archaea), the point being that there were organisms before that, but it's difficult to know what they were like because evidence from phylogenetics pretty much stops at that point. Origins of life researchers study what came before modern biology. I could add this explanation to the question, and probably should. This will make it clearer, but also longer. $\endgroup$ – Nathaniel Jan 3 '15 at 14:23
  • $\begingroup$ I wish I could make it clearer somehow, because I haven't been able to get the central point across to you. The question really really isn't just asking for functions that have evolved, it's asking for functions that have evolved under a very specific environmental context. I feel that if you understood this you would have much less of a problem with it. It's long because it's trying to express a difficult concept precisely, and the examples are there to illustrate that concept. I would make it half the length and ten times as clear if I could, but I honestly don't know how. $\endgroup$ – Nathaniel Jan 3 '15 at 14:24
  • $\begingroup$ But the main point of this meta question is this: should it really be necessary for me to do that? Some readers understood the question perfectly, and one of them might be able to answer it. We all have different backgrounds, and the terminology of my field is clearly such that it's hard for you to understand. But is that by itself enough to shut down the question? I would say no. It's inevitable that some questions will be hard for some readers to understand, especially if you want more experts on the site. If we use our close vote privileges on them the site will be deeply impoverished. $\endgroup$ – Nathaniel Jan 3 '15 at 14:25
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    $\begingroup$ @Nathaniel "should it really be necessary for me to do that?"... Yes, because if someone else is interested in the problem then it would be helpful for them too. That is the point of SE. Same goes for answers- it is better to explain the answer and include all necessary points. Moreover you may get a good answer from someone who is not familiar with the terminologies of your specific field. Terminology is afterall just a word and not an entire concept (same concepts can have different terminologies as you might know, having worked in interdisciplinary areas) $\endgroup$ – WYSIWYG Jan 3 '15 at 14:38
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    $\begingroup$ @Nathaniel You said some people understood the question but you still didn't get your answer right. That means something is missing. And trust me when I say that the question was closed not because nobody understood the concept. I would rather say that the precise question was unclear. As it was worded it seemed like you were asking for a list of examples. Clarifying the background of the question is important but in a precise way. At least enough for a PhD level person to understand. Just like you do in the introductory slide of your presentation. $\endgroup$ – WYSIWYG Jan 3 '15 at 14:43
  • $\begingroup$ @Nathaniel Would you add these points (post LUCA) in your question? Would you mind if I make some attempts to shorten the question (you can rollback if you find it unsuitable) $\endgroup$ – WYSIWYG Jan 3 '15 at 14:50
  • $\begingroup$ to be honest I'd prefer it if you didn't. I'm convinced that you haven't understood the question, and it wouldn't really be appropriate for you to edit it under such circumstances. But I can't stop you, and of course I can always roll it back, so knock yourself out if you must. $\endgroup$ – Nathaniel Jan 3 '15 at 14:53
  • $\begingroup$ I will edit the question further to include that point and others, and hopefully to make it concise as well. But not today. $\endgroup$ – Nathaniel Jan 3 '15 at 14:57
  • $\begingroup$ I agree that it's good if a question is understandable to as wide an audience as possible. I always strive for this. But I think it's absurd to say it has to be understandable by all readers. There are questions on Stack Overflow that are expressed in terms that I don't understand because they're about obscure languages that I don't use. Should I vote to close them? Obviously not. They will be helpful to people who have questions about those languages in the future, just as my question and its eventual answer will be helpful to other researchers in origins of life. $\endgroup$ – Nathaniel Jan 3 '15 at 15:03
  • $\begingroup$ I believe the reason my question is currently unanswered is not that it's unclear. Rather, it's because it's a difficult, research-level question. Most likely there isn't anyone currently on the site who can answer it, but if the site is successful then in the future there will be someone here who can. (Do you have many experts in evolutionary biology yet?) I'm not in a hurry and can wait. $\endgroup$ – Nathaniel Jan 3 '15 at 15:06
  • $\begingroup$ If you do edit my question it would be nice if you'd do it during waking hours, Japan time. I'm going to bed now, and will be up in another eight hours or so. $\endgroup$ – Nathaniel Jan 3 '15 at 15:12
  • $\begingroup$ @Nathaniel Well.. you don't seem to understand what I am trying to say. Anyways good night. I am not editing anything. Do as you please. End of discussion. $\endgroup$ – WYSIWYG Jan 3 '15 at 16:49
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    $\begingroup$ @Nathaniel - I think you are ignoring what other professionals - biologists - have told you. Questions are not closed because people don't know the answers, yet you cling to this as an excuse to believe your question is clear. It's not. I won't tell you what makes a clear physics question. Please don't try to sell us on the idea that only because it your question is "so complex" that we biologists cannot understand it. In your now-deleted post, there were plenty of bad questions which you decided were good, and you were wrong. So is it the case here as well. $\endgroup$ – anongoodnurse Jan 4 '15 at 6:53
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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.

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    $\begingroup$ This is the thing though: I truly cannot understand the assertion, made by you and several others, that this question is broad. It is not. It is asking for something so specific that it might not exist at all. (But it might, which is why I'm asking the question.) Yes, obviously I know how to do bibliographic searches, but I also know when I'm beaten by a lack of knowledge of the field and the terminology surrounding it --- when it's time to ask an expert, in other words. $\endgroup$ – Nathaniel Jan 2 '15 at 10:43
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    $\begingroup$ I get that you can't answer my question, but that doesn't make it off topic, it just means you personally aren't in a position to answer it. This site won't get far if questions get closed because five people don't know the answer. To answer your query, my background is mostly computer science and statistical physics, with a little chemistry and some population ecology. At a rough guess I'd say about 50% of origins of life researchers are biologists, maybe 30% chemists, and 20% other, including me. It's a diverse field. $\endgroup$ – Nathaniel Jan 2 '15 at 10:47
  • $\begingroup$ @Nathaniel - Honestly, it's not a case of five people who don't know the answer voting to close, and that, I believe, is an oversimplification you can recognize. To you, in another post, the question What are the tissues affected by thyroid hormone called? is a straightforward, specific question. To me, I cringe, it's so... I don't want to be unkind, but it's a very silly and meaningless question, since thyroid hormone is necessary in nearly every tissue. So what's the answer? Living tissue? Thyroid-sensitive tissue (so ubiquitous as to be nearly meaningless)... $\endgroup$ – anongoodnurse Jan 2 '15 at 11:12
  • $\begingroup$ ...We also differ in our approaches to investing in a site. To me, it's more than seeing how my questions are answered (I have yet to ask one here). If I like the field, I'll check it out. If, after a while, I like the site, I'll start contributing as I get to know the site better. I contribute by answering questions. I don't expect anyone to give me an answer (much less to owe me one) if I haven't given my share. Good questions are a contribution to a site. But you have to know the field to know how to ask good questions. It's a bit of a Catch-22. $\endgroup$ – anongoodnurse Jan 2 '15 at 11:19
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    $\begingroup$ @Nathaniel This site only develops with contribution - from you, me and everybody else. Asking well received (and understood) questions takes some effort, and it's not up to you to say "I will only participate when you receive my questions well". It is also up to you to formulate questions in a way that they are understandable. With that, you are also more likely to receive an answer. Also changing the policy here invokes interaction and participation, this will not happen by itself. So if you are interested, you are as welcome as any other user here. $\endgroup$ – Chris♦ Jan 2 '15 at 11:39
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    $\begingroup$ @anongoodnurse Regarding the thyroid hormone question: perhaps the community would be well served by answering such a question as you just have instead of closing it. Just a thought; I can also understand why some would wish to close it. $\endgroup$ – canadianer Jan 2 '15 at 21:09
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    $\begingroup$ @canadianer - "Since thyroid hormone is necessary in nearly every tissue, what's the answer? Living tissue. Thyroid-sensitive tissue (so ubiquitous as to be nearly meaningless)." Is not an answer I'd be likely to give. There is a difference in opinion on what is a good question, what kind of questions one wants to encourage. The community has to decide that. If the community decides to answer every question without regard to research effort or basic understanding, then these questions will get answered. $\endgroup$ – anongoodnurse Jan 2 '15 at 23:19
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    $\begingroup$ @anongoodnurse The answer could be that since thyroid hormone affects nearly every tissue, no general term exists or is used in common practice. $\endgroup$ – canadianer Jan 2 '15 at 23:28

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