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The question

Presumably, biophysics questions run a wide range from those that are primarily biology questions with a little physics input to those that are primarily physics questions applied to a situation that appears in a biological processes or system

And presumably some fraction of them are on-topic for the Physics.SE site.

This question is soliciting reasoned and explained opinions about what kinds of questions are definitely on-topic, off-topic and living in a fuzzy gray area.

Proposed texts for the summary would be one (good) way to condense your thoughts, but are not required. For reference, the current tag summary reads

The use of methods from the physical sciences to aid in the study of biological systems. Note that biophysics questions are only allowed if they are mainly about physics.

Background

After a recent conversation concerning the need for or utility of possible Biophysics beta site we received a question on the main site concerning the mechanisms of protein action (and a few other issues). A subsequent informal poll of the chat room revealed surprising diversity of opinion on the matter including

Note that this meta-question is not mainly about the place of post 227647 on Physics SE, but about the broader criteria for deciding such things.

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    $\begingroup$ One thing that I think is important to note (but not sufficient to constitute an "answer" to this question) is that I think that physics-based questions that require a lot of biology background should be firmly on-topic! Just because we don't (yet?!) have the people to deal with these questions does not mean they're not about physics (what prevents us from closing all questions that are only accessible/answerable to very few people otherwise?). $\endgroup$ – Danu Jan 6 '16 at 21:13
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    $\begingroup$ In my view the question, at least in its current form, is unquestionably on topic. I'd like to contribute to a discussion of how to determine what's on topic in this area, but I'm unable to understand the objections to this one. (Unless they're referring to an old version of the question that was much less clear?) The only ones that make sense are the suggestions that it would be better off on chemistry, but those are misguided. Yes, covalent bonds are part of the explanation, but the rest of it is very far from what chemists study. It really is a basic question in pure biophysics. $\endgroup$ – Nathaniel Jan 11 '16 at 9:35
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This is how I see things in the world of biophysics out there. The work (and fun) of biophysicists is to ask questions about biological systems. In their answers, they use (and build from) all the experimental and theoretical tools that the other physicists use in the many other physical disciplines. In this view, a "biophysics question" cannot be about physics, it has to be about a biological system. I'm not talking here about a question on this site, what I mean is that the ultimate object of a biophysical question (or of a biophysical research) is a biological system, not a physical principle, otherwise you have to drop the "bio". The biophysical answer, on the other hand, is (and has to be) deeply rooted in the way a physicist reasons, and this makes the difference between biophysics and biology. The difference is more in the answer than in the question.

A question like How does the ribosome work? cannot be simply categorized. A categorization is easier to do for the possible different answers, which can be more chemistry-oriented (catalysis of new peptide bonds), biology-oriented (protein synthesis by reading a mRNA template), or physics-oriented (nano-machine at low Reynolds that moves on a periodic potential).

How to translate this to Physics SE? From what I said, I have to conclude that the tag description

"Note that biophysics questions are only allowed if they are mainly about physics."

is a contradiction. Like "Note that relativity-related questions are allowed only if about semiconductors", if I may exaggerate. But I think it is understandable what that means: we want to focus on physics, not biology, which is reasonable.

So, my 2 cents:

Note that biophysics questions, which have a biological system as an object, should both be answered and answerable from a physics perspective, using descriptions, modeling and tools from physics

With this, I hope that people with right to vote "off topic" will recognize that "how the ribosome works?" is surely answerable by a physicist, therefore absolutely on topic, and potentially very interesting for this site.

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  • $\begingroup$ Very much the tenor of comments I was hoping to attract. Thanks. $\endgroup$ – dmckee Jan 13 '16 at 23:22
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I just took at look at the question linked in this post, version 4. I think the question was closed because it's vague and too broad, not really because it's about biology. I think this happens a lot on our site and warrants discussion.

Problems with the example post

Consider the first three paragraphs of the post:

Let's, for example, take a ribosome. It is an enzyme that is in turn just a molecule that must follow the laws of physics.

Correct me if I'm wrong, but it can be looked upon as a molecular machine made up of several pieces. What exactly makes those pieces work together?

Why does the ribosome bind to a strand of RNA? Is it just the shape and electric charge or is it something more? Once the ribosome is bound to a piece of RNA, how does it move?

There are four question marks by the end of the third paragraph:

  1. "What exactly makes those pieces work together?"
  2. "Why does the ribosome bind to a strand of RNA?"
  3. "Is it just the shape and electric charge or is it something more?"
  4. "Once the ribosome is bound to a piece of RNA, how does it move?"

Having multiple questions is alone a problem. When faced with multiple questions, a would-be answer writer has to read, understand, think about, formulate answers for, and then write answers for multiple questions. If the probability that a given reader can do those things for one question is p << 1, then the probability that a given reader can do them for four questions is p^4, which is absolutely tiny. This puts a reader at a disposition to regard the question as unanswerable.

Now, a deeper problem is that the questions bounce back and forth from specific and physics-oriented to broad and biology oriented. Questions #1 and #2 are very broad and sound biology-ish. A typical physicist probably feels that only a phenomenological bio or so-broad-as-to-be-useless physics answer can possibly suffice. This, puts the physicist at a mind to vote for closure.

Then in question #3 we get physics: "Is it just the shape and electric charge or is it something more?". That is a physics question. Or at least it suggests one. We could rewrite the entire post around that one question:

Ribosomes perform complex tasks in the organism, but in the end they are just molecules and therefore governed by the laws of physics. What physical principles are the most crucial for understanding how a ribosome is able to function as it does? To choose a specific example, is electrostatics enough to explain why a ribosome sticks to a strand of RNA?

Unfortunately, we then get question #4: "Once the ribosome is bound to a piece of RNA, how does it move?" This is again vague and broad. Does the asker want an explanation from the bio point of view or a purely electrodynamical description?

Why (I think) the post was closed

Vague, broad posts like this invite closure because they're hard to answer. As they translate to "how does X work?", they invite too many possible levels of scope. Posts like this could reasonable be closed as "too broad" or "unclear what you're asking". However, I think its psychologically easier for readers to perceive a question as possibly ok for another audience rather than stick their chin out and tell the OP that their question is bad. Hence, we see a lot of questions closed as "off topic" where "too broad" and "unclear what you're asking" would make more sense.

At least, that's my guess. This is not a great situation because "off topic" tells OP to go somewhere else, rather than learn how to ask questions better. We definitely want better questions more than we want to turn people away, so...

What do to

  1. Use "off topic" only as a last resort. Prioritize close reasons which help OP learn to ask better.

  2. If you can, edit the post to zero in on the relevant question. The example I pose above is probably too big of an edit, but a comment can help OP get there. It may also be ok to make a substantial organizational edit and post a comment reminding OP that they can roll it back if it misses the mark.

So what about the place of biophysics?

I think interdisciplinary questions get closed a lot because, as illustrated above, it's easy to lose focus and put readers in a state of mind where they feel like the question gets so large that a good physics answer can't address it. I think biophysics questions in the vein of my example rewrite given above are solidly on topic. So, with all this said, I really think the only legit answer here is that we need to see more good biophysics questions before we can even consider writing down explicit descriptions of which ones are and are not on topic.

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