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Proposal: Synthetic Biology

I'd like to know what the response is to the elephant in the room: why do we even need a SynBio SE in the first place? Researchgate already provides a Q&A site for questions that researchers have, and it already contains many high-quality answers. In addition, Synthetic Biology, by definition, is a subset of Biology, so shouldn't all questions just be asked in the existing Biology Stack Exchange? For questions that are more mathematical in nature, can't they be asked in the Bioinformatics stack exchange?

The area 51 FAQ provides the following guidelines for this question:

Site X should be subsumed by site Y if:

  • Almost all X questions are on-topic for site Y
  • If Y already exists, it already has a tag for X, and nobody is complaining
  • You're not creating such a big group that you don't have enough experts to answer all possible questions
  • There's a high probability that users of site Y would enjoy seeing the occasional question about X
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My take on this is two-fold:

  • First, SynBio is an extremely cross-disciplinary pursuit. This means that often the answer to a question doesn't fall into a category neatly.

    For example, my answer to your example question about differences between GFPmut3, EGFP, and sfGFP would be to point people to GFPmut3, despite the fact that it's an objectively worse fluorescent protein, because results using it are more likely to give compatible units for data fusion and because it's definitely out of patent, where I'm not certain of that for sfGFP. Notice that this answer tightly links concerns in biology, computer science, and IP. Many SynBio answers will be similarly complete.

  • Second, in my vision of a SynBio.SE site, the questions would be mainly from practitioners (at all levels), focusing on how to do things. This is complementary to Bio.SE, which has some "how", but is mainly focused on more natural-science "what is this?" and "why is this?" questions. The difference, in my mind, is like that between Electronics.SE and Physics.SE.

    Likewise, I believe many biology questions about the nature of natural systems would not be appropriate for a SynBio.SE. Here's an example pairing:

    Off-topic, transfer to Bio.SE: "I am investigating therapy for [disease]. The literature suggests that [Gene X] is important, but I don't understand the model. How does [Gene X] contribute to [disease]?"

    On-topic, answer: "I am investigating therapy for [disease] by up-regulating [Gene X]. How do I limit off-target impacts of my CRISPR delivery vector?"

  • Finally, other Q&A sites like ResearchGate don't support the high level of focus and curation quality that the StackExchange model supports.

In short, I believe there's no site that currently covers SynBio well. This is affirmed by the discussion on Meta-Bio.SE before this proposal was launched.

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    I really like the comparison between Electronics.SE and Physics.SE; having communities to support both engineering and natural sciences questions seems great – tessafyi Feb 3 at 19:56
  • bioinformatics.stackexchange.com is another comp to consider. They permit a lot of "how do I do this technical thing with this tool" questions that we frown upon at Biology. Questions about interpreting Bioinformatics-based output etc is still on-topic on Biology, as are any other bioinformatic questions that are about the underlying biology or scientific basis of techniques, but questions about the operation of particular software tools are not. I don't feel like we've had any conflict with Bioinformatics, though other overlaps like Data Science/AI/CrossValidated have had some. – Bryan Krause Feb 22 at 22:14
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    @BryanKrause Absolutely, and I expect there will be some overlap, e.g., "How do I perform this sequence-verification task on my plasmid" sorts of question. I believe that nearly all of the definition questions for the SynBio proposal, however, are ones that cross into areas that wouldn't make sense on bioinformatics.SE. – jakebeal Feb 22 at 22:22
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    @jakebeal Yeah I meant it more that in some ways Bioinformatics and Biology have a relationship a bit like Electronics and Physics. It seems like this site can be another Bioinformatics with respect to Biology; how Bioinformatics and SynBio coexist is a separate issue that I don't feel qualified to opine on. In practical issues, I'd say we run into more issues with Med Sciences and Psych & Neuro as far as question overlap (the main issues being simultaneous cross-posting by new users, and cross-site dupes where a question has already been asked and answered elsewhere). – Bryan Krause Feb 22 at 22:25
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I'd like to add to the other answers a comparison with "Ask Ubuntu SE" and "Unix SE". There has been discussion for years on whether these two Stackexchanges should be merged, as Ubuntu is a UNIX OS. However, the response from the Ubuntu community when asked if they wanted to be merged is, as far as I can tell, always negative: see here and here.

The second link has a good suggestion for why this is:

So, Ubuntu, Linux, I get it, it’s clearly not the same thing. If you love Ubuntu, we have a site for you. If you love Linux and Unix, we have a site for you. (If you’re looking for work in Linux, we have a Linux Jobs site for you, too). A Stack Exchange can’t work without a community that loves a subject, and love is very… specific.

I think we have a similar situation here with SynBio. Even for questions that could be asked in the Biology SE, if users want to ask the SynBio community specifically, they need a SynBio StackExchange. At the end of the day, Area 51 is about testing whether a new community is needed/wanted, so we will see!

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    It's interesting to note that Ask ubuntu has actually been there since before the Unix&Linux SE! – Nike Dattani Feb 9 at 4:38
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To me it's because in platforms like SE you can not cover al chemistry nor biology in a single place. In the information era we would like to filter and focus our attention in delimited fields, like SynBio. Synthetic Biology even has its own nomenclature and metaphors so we talk in terms of genetic circuits, the repressilator, PoPs, MEFL, connect this NOR gate using C4 and C12 and we use SBOL. This makes easier the communications between synthetic biologists so we need more places like SE to talk this language and advance the field as a collective.

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