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We have decided to see if there is sufficient critical mass to start a complementary synthetic biology SE site (by analogy, "Electronics.SE" to this site's "Physics.SE"). If interested, please follow the proposal in Area51.


Update #2: The Area51 Synthetic Biology proposal is now in its commitment phase. Most of the community coming in are from outside of StackExchange, so we particularly want to invite experienced StackExchange folks to commit and be able to help show the newly-arriving experts the ropes!


Folks from iGEM are looking to either create or join a persistent Q&A resource for synthetic biology students needing help with protocols, genetic design, etc. Bringing a community to this site is one of the possible approaches under consideration.

I've been poking around this site the last few days, however, and most of the questions that I see here are of a much more popular science or "what's this thing in my back-yard" nature. I've also seen a rather negative response to what seemed to me a fairly straight-forward question about scale-up. Together these make me wonder whether this community would consider such questions to be de facto out of scope.

Would this site welcome an influx of technical questioners and answerers focused on the pragmatics of practicing synthetic biology?

Some potential example question titles:

  • "GFPmut3, EGFP, sfGFP... does it matter which GFP I use?"
  • "Failing to get colonies on a MoClo assembly. How to debug?"
  • "If I adapted a sequence found in a paper, can I share it under the OpenMTA?"
  • "Which assembly protocols are good to run on an OT-2?"
  • "What do I need to do to adapt an E. coli part for B. subtilis?"
  • "How can I express gRNA from a sensor using a Pol II promoter?"
  • "Are there any high-throughput metabolite assays for plate readers?"
  • "What are the most common sources of error in preparing cell-free extract?"
  • "Why are my OD numbers going up rather than down when I titrate my calibrant?"

Added on 1/26: committee members would appreciate comments on the scope of these questions (assuming they had evidence of work, etc.):

  • "I have attempted to simulate the growth of Vibrio natriegens on different media using dynamic FBA, but I'm not sure if the output I'm getting is biologically-relevant or if it's an issue with my code, can someone have a look at it for me?"
  • "I have attempted to model the growth of Vibrio natriegens on different media as a system of ODEs, but I'm having some difficulty understanding the mathematical notation in this paper that did something similar, can someone help me?"
  • "I want to model the growth of Vibrio natriegens on different media, would it be more appropriate to use a system of ODEs or dynamic FBA?"
  • "I want to model the growth of Vibrio natriegens on different media, and have designed a system of ODEs. Is this more quickly solved in Python or Matlab?"
  • "I'm want to integrate a DOE I ran to test different growth conditions in Vibrio natriegens with a system of differential algebraic equations that I have used to model my bioreactor, would Bayesian parameter estimation be applicable here?"

Would these also be appropriate here, or are they things that would have to go to Bioinformatics.SE or somewhere else?

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  • $\begingroup$ It would be helpful if you could give us several example questions (more is better). Also, have you taken the tour and read through the help center to get a good grasp of what's on-topic and what isn't? I would also advise you to not take the word of any single community member as representative of the entire group. We have some particularly grumpy, restrictive participants, and some that would let in anything at all. $\endgroup$ – MattDMo Jan 24 at 1:27
  • $\begingroup$ As for the question you linked to here, I think most of the OP's questions could have been answered in the Wikipedia article you referenced at the very beginning of your answer, so the downvotes and close votes were likely (at least in part) motivated by the lack of research. $\endgroup$ – MattDMo Jan 24 at 1:33
  • $\begingroup$ @MattDMo I've added some potential example question titles $\endgroup$ – jakebeal Jan 24 at 1:48
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    $\begingroup$ @MattDMo Also, yes, I've read the topic definitions; I'm trying to figure out how they are de facto interpreted by this community. $\endgroup$ – jakebeal Jan 24 at 13:02
  • $\begingroup$ I don't know the community, but these look like solid, interesting questions I'd love to see answered well. The vaccine question was broad, something you could write a book about and still miss something to be introduced tomorrow (...can we put a T7 site in a LAMP primer and brew a new mRNA vaccine straight from a positive test result, anyone?) - I wouldn't infer a general principle from it. $\endgroup$ – Mike Serfas Jan 24 at 16:00
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    $\begingroup$ Personally I think there is a dearth of good, technical and interesting questions here. If the questions conform to the sites guidelines, I would love to see them here. $\endgroup$ – user438383 Jan 24 at 16:49
  • $\begingroup$ I recognized your name and didn't realize most of your contributions here are so recent - I now realize that's because you're so active at Academia. Welcome to Biology.SE! $\endgroup$ – Bryan Krause Jan 25 at 1:48
  • $\begingroup$ Thank you, @BryanKrause; as you know, I'm pretty familiar with the SE model in general. I also know that every different community has its own approach to that model, however, which is why I've been testing the waters over here to help bring more useful information into my committee's decision-making process. $\endgroup$ – jakebeal Jan 25 at 1:52
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    $\begingroup$ Indeed, thanks for asking the question ahead of time. Do you have an idea of the extent the volume would be if the answer were 'yes'? $\endgroup$ – Bryan Krause Jan 25 at 2:20
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    $\begingroup$ Unclear. On the one hand, iGEM has around 300 teams per summer, so if a lot of them started using the resource, it could easily be a couple dozen questions per day throughout May through September. On the other hand, students aren't great at using resources, and despite best efforts we might end up with only a handful of questions at all. Beyond iGEM, if this turns out to become a good general use tool for greater synthetic biology community, the rate could gradually swell to a higher level at the graduate level and above, though that would likely be a much more organic process. $\endgroup$ – jakebeal Jan 25 at 2:44
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    $\begingroup$ If we do try to bring folks in, I think we'd likely want to try to seed things by having committee members model with a number of FAQ-style questions. $\endgroup$ – jakebeal Jan 25 at 2:49
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One point I'd like to emphasize is that this is not a tutorial site or discussion forum, which many of your your example questions seem to assume. I think most of them could be edited into decent shape:

  • "GFPmut3, EGFP, sfGFP... does it matter which GFP I use?"

    What are the differences between GFPmut3, EGFP, and sfGFP in the context of [my kind of experiment]?

  • "Failing to get colonies on a MoClo assembly. How to debug?"

    Failing to get colonies on a MoClo assembly after 3 tries. Are there issues with my protocol [attached]?

  • "If I adapted a sequence found in a paper, can I share it under the OpenMTA?"

    Off-topic. Maybe try Law.SE...

  • "Which assembly protocols are good to run on an OT-2?"

    I'm trying to scale up X, starting with this protocol. Can it easily be adapted to an OT-2 robot?

  • "What do I need to do to adapt an E. coli part for B. subtilis?"

    I'm adapting an E. coli part for B. subtilis, but X happened. Why is that, and how can I get Y instead?

  • "How can I express gRNA from a sensor using a Pol II promoter?"

    I found this protocol for expressing gRNA from a sensor using the Pol II promoter, but it's pretty old and requires [this unavailable reagent/this undesirable condition]. What can I do to modify it?

  • "Are there any high-throughput metabolite assays for plate readers?"

    Google and Google Scholar are your friends here.

  • "What are the most common sources of error in preparing cell-free extract?"

    My cell-free extracts have highly variable activities and yields. Are there any tweaks I can make to my protocol [attached]?

  • "Why are my OD numbers going up rather than down when I titrate my calibrant?"

    My ODs are increasing when I titrate my standard. This is exactly how I'm doing it, and I tried making these changes, but the results are the same. Where am I going wrong?

Starting to see a pattern here? Chatty, open-ended, truly opinion-based, and/or poorly researched questions are not on topic here, but specific questions that have the appropriate context (detailed protocols, prior research) looking for specific answers are fine. Seeking fact-based, expert opinion is okay, as that's why we (answerers) are here, but asking in such a way that answers are likely to just be personal opinions is not.

The expectation is that you put as much effort as possible into researching and answering your own question, including running the experiment multiple times, then collect all that information in a readable format and present it to us. Read the following Help Center pages over and over:

All users are expected to take the tour and be familiar with everything in the help center. Doing all of this ahead of time will prevent innumerable headaches down the line.

So, to answer your original question, yes we would welcome additional technical questions about synthetic biology, as long as they are in line with the site's standards and rules. I'll say it again, this is not a tutorial site or discussion forum, so please ensure your community is aware of that up front.

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  • $\begingroup$ Overall I agree with both theforestecologist's answer and your answer here (and of course there is a lot of overlap), but I agree more closely with how this answer addresses each of the example questions suggested. $\endgroup$ – Bryan Krause Jan 25 at 1:47
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    $\begingroup$ +1 Thanks for taking the extra effort to rewrite the questions for the OP -- very helpful. $\endgroup$ – theforestecologist Jan 25 at 1:50
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DISCLAIMER: These are my personal (albeit informed) opinions. I would wait for additional comments, answers, and up/down voting to see what a more general community consensus might look like.


To me, the short answer is "yes, if..."

Let me explain:

Yes

Synthetic biology would certainly fall under the realm of acceptable topics here.

  • In fact, ~88 posts have already been labeled with the tag as of writing this answer.

We also welcome student participation on our site. From our tour:

Biology Stack Exchange is a question and answer site for biology researchers, academics, and students

If...

It sounds like most of the "influx" of posts you're referring to will come from students, which might put some members on high alert due to the many low-quality posts we get globally from some students.

As I mentioned above, we do welcome students here, but we do so with the expectation that they be held to our site-wide high standards.

  • Again from the tour, "we're working together to build a library of detailed answers to every question about biology." Our focus is not to teach novices nor to answer homework questions. (See our homework policy and many meta discussions on the topic).

  • We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way.

In summary, we do not need an influx of basic questions that can and should be answered using intro textbooks or Wikipedia. Such questions should be researched by students on their own. However, if these students still find something confusing and can explicitly describe their sincere personal efforts to understand a difficult topic, we'd be happy to help them understand. :)

Of course, such students should come to understand how our site works via the tour and help-center, and they need to follow our other guidelines for writing good-questions and types of questions to avoid asking.


I'd like to react to how I think some of the example questions you've provided would be received here:

  • "GFPmut3, EGFP, sfGFP... does it matter which GFP I use?"

    • Off-topic: asking for opinion-based answers.
  • "Failing to get colonies on a MoClo assembly. How to debug?"

    • Ok if asker provides context, what's been tried, etc.
  • "If I adapted a sequence found in a paper, can I share it under the OpenMTA?"

    • Off-topic: asking for opinion-based answer AND relating to professional behavior vs actual biology.
  • "Which assembly protocols are good to run on an OT-2?"

    • Closed as being too broad, not demonstrating prior research effort, and "good" suggests the the OP would be seeking opinion-based answers (not allowed).
  • "What do I need to do to adapt an E. coli part for B. subtilis?"

    • OK if asker explicitly demonstrates prior research effort in their post (i.e., how they already tried to answer their own question). I think the broad "what do I need" design of this question would suggest lack of such research effort. A better post would question about some particular aspect of some protocol.
  • "How can I express gRNA from a sensor using a Pol II promoter?"

    • OK if asker explicitly demonstrates prior research effort in their post (i.e., how they already tried to answer their own question). My guess is that this "how" question might not demonstrate such effort, but a question honing in on some specific aspect of such a protocol might be better. (alternatively, if such a protocol is not standard, the question could be reformulated to demonstrate how they've gotten to asking this question and suggesting (ideally cited) attempts to do something similar)
  • "Are there any high-throughput metabolite assays for plate readers?"

    • Needs to explicitly demonstrate prior research effort (how they tried to answer their own question).
  • "What are the most common sources of error in preparing cell-free extract?"

    • Feels quite broad to me. Broad questions often indicate lack of prior research effort. More appropriate might be to hone in on a specific type of error and ask questions about something that is still confusing them.
  • "Why are my OD numbers going up rather than down when I titrate my calibrant?"

    • Needs to explicitly demonstrate prior research effort (how they tried to answer their own question) and to provide adequate context.

Again, these are my personal (and somewhat superficial) thoughts, so I welcome others to weigh-in further...

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    $\begingroup$ Interesting --- your responses, along with the other things I've seen so far on the site, is leading me to believe that synthetic biology really is a mismatch for Bio.SE. It seems like Bio.SE is very focused on the scientific "what" and "why" aspects of biology and doesn't have much space for the "how" of bioengineering. A comparison might be Physics.SE vs. Electronics.SE. You go to the first to ask how a resistor works and to the second to ask which one to use in a particular circuit. $\endgroup$ – jakebeal Jan 24 at 20:11
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    $\begingroup$ I think "how" questions are ok actually (more than 10k such questions already exist on our site). It just matters how they're asked. As I describe in my post, we aren't in the business of just telling people how to do something because they asked. We want each question asker to ask informed questions that demonstrate prior effort to answer their own question. So very broad/general "how do I do this" is not really ok, but "I need to do W, and my own research/googling suggests X is a valid approach. After reading Y I don't understand Z about X" is a much preferred starting place. $\endgroup$ – theforestecologist Jan 24 at 21:23
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    $\begingroup$ I'd echo theforestecologist on 'how' questions. "How" as in "write me a tutorial" isn't a good SE format question on any SE site. However, there are lots of very useful questions that help with the steps in a "how" process. $\endgroup$ – Bryan Krause Jan 25 at 1:45
  • $\begingroup$ @BryanKrause Maybe the size of the "how" is the key distinguisher? I keep thinking of all of the extremely useful "recipes" one finds on StackOverflow like "How can I reverse a list in Python?". So "How do I calibrate my flow cytometer?" is too big, but a good one could be "How do I figure out which peaks I'm looking at when calibrating to MEFL with SpheroTech RCP-30-5A beads? My channel is adjusted for weak fluorescence, and I think some of the high peaks are off scale." $\endgroup$ – jakebeal Jan 25 at 3:02
  • $\begingroup$ @theforestecologist A lot of the material we're interested in helping people get at doesn't have any good resources online right now. It's too operational for textbooks and too "simple" for papers, so mostly its essentially passed around by oral tradition within laboratories and between collaborators. Thus, the interest in trying to organize an SE-style location for pooling information about common problems and their solutions. $\endgroup$ – jakebeal Jan 25 at 3:06
  • $\begingroup$ @jakebeal Yes; some "how"s implicitly demonstrate a bit of surrounding work. I don't know your field, but to me it's the difference between "how do I drive a car?" and "how do I signal my intention to go straight when entering a 4-way one-lane roundabout?" StackOverflow itself is kind of difficult source material because I feel they accept a broader "how" than the sub-sites do sometimes, and yet this makes sense because of their overall breadth. For example, someone who wants to reverse a list in Python isn't necessarily someone who doesn't know how to reverse a list in general. $\endgroup$ – Bryan Krause Jan 25 at 3:24
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    $\begingroup$ The rejections described above sound like persuasive reasons for anyone to abandon StackExchange, but can you explain how they relate to the guidelines cited? I see guidelines against requests for opinions where every answer is valid, against personal medical advice and philosophical issues, and a page offering recommendations to help improve the chances of receiving a useful answer. I don't see anything written there saying that research is mandatory or requests for advice based on facts and experience are off topic. $\endgroup$ – Mike Serfas Jan 29 at 1:25

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