My overall experience has been unfriendly and negative. Lots of negative reinforcement, no positive reinforcement.
It looks like you have seven active answers and one question. These all have a net positive score. Your one question has an answer, though there are no votes on this answer (if it is helpful, you could upvote it; if you feel it sufficiently answers your question, you can mark it as an accepted answer). Clearly you've had some negative experiences outside of these posts, perhaps with seeing questions by others that are closed, but I don't think it's fair to say there is no positive reinforcement directed at your contributions here.
Close votes and explanatory comments
There are some details about what it means to close a question here: What is a "closed" or "duplicate" question? Users with sufficient reputation can vote to close questions. Close votes, except those by moderators, are not binding, they're just votes. It takes 5 community members voting to close a question for it to actually be closed. Closed questions don't disappear, and some can be edited and later reopened, closing is just a way to prevent answers in the meantime.
Users do not need to explain their close votes, but some choose to. Explanations for close votes don't set site policy, it's just one user explaining why they've voted the way they have. Why do some users feel a need to explain their votes?
Sometimes, question askers get frustrated because they don't understand why people are voting to close their question. They may write angry comments like "Why are people voting to close?"/"Close voters - explain yourself!" (perhaps this is also just a direct question and maybe it's not fair to call it 'angry', but I can say in my experience with SE that often these forms of comments come paired with some angry words and expletives). Some users may see these comments on other posts and choose to preemptively explain their own votes, trying to help the askers understand their action.
Other times, when people try to explain their votes the user reacts aggressively towards the explanation. Name calling and accusations of censorship or bias are common. Sometimes these responses betray that the user has not attempted to learn the site guidelines in the Help, especially https://biology.stackexchange.com/help/dont-ask and https://biology.stackexchange.com/help/on-topic As a result, a lot of people just vote quietly without comment.
For me personally, since I'm a moderator here my own close votes will unilaterally close a question. Sometimes I feel a question should be closed, but I don't feel it's clear cut enough to use my vote. In that case I will sometimes leave a comment instead. I'm open to feedback on these comments if anyone feels I am misrepresenting the site scope or being unfriendly.
Questions that are and are not on-topic for Biology.SE
The scope of the site is determined through discussion on Meta. If one would like to change the scope, the way to do so is to raise a discussion on Meta. Interpreting the site scope is not always straightforward, and different users may interpret the site scope differently and therefore vote differently on questions. I think it's reasonable to expect some difference of opinion on these things, and to expect that not everyone will vote the same way. That lack of clarity can certainly be frustrating, but I don't think there is any alternative in a community of individuals who think independently.
BIOLOGY vs Biology.SE
it seems the biology sub frequently decides, inaccurately and inconsistently, that some technical questions about biology research are "not biology".
Biology.SE is not the only scientific site that excludes questions about broader technical application of the field. Electronics.SE is an example with respect to Physics. In general, a SE site's name is just a label that serves as a general colloquial description. It is not meant to indicate some taxonomic scope. Though one can argue biology is just applied chemistry, most biological questions aren't on-topic at Chemistry.SE, only those that relate to basic chemistry. Same on down the line for Physics and Math. Something can be reasonably argued to be within the scope of BIOLOGY and yet outside the scope of Biology.SE.
It's certainly difficult to define scope rigidly, but ultimately actions like "closing a question" are rigid and binary: a question is closed or it is not.
Synthetic biology and bioinformatics
The Biology.SE site scope in the Help includes:
questions about techniques in a biological or biochemical laboratory
as on-topic. If one interprets the second statement broadly, it indeed seems that many techniques in fields like bioinformatics and synthetic biology would be on-topic. However, there is also a second clause that states:
Questions on interdisciplinary subjects like bioinformatics are also welcome, as long as they focus on the biological part of the subject.
For strictly bioinformatics questions, I think we've mostly settled as a community on where the lines are. There is a separate site, Bioinformatics.SE, where many of these questions are on-topic. There is a structural biology tag there with a handful of questions.
For synthetic biology, we haven't had a lot of those questions historically. Some may also overlap with Bioinformatics. Some users here with experience in the broader SE community wondered about changing that, and started a Meta discussion here: Would this site welcome an influx of technical synthetic biology Q&A?
Feedback from the community was, if it's fair for me to summarize, that while many of the suggested questions are perfectly reasonable here (or could be modified to fit), others weren't a great fit. As a result, there is now a Synthetic Biology site incubating at Area51. If this site makes it to Beta, I see it filling a similar niche to Bioinformatics but in the synthetic biology space.
What to do now?
Besides supporting the SyntheticBiology.SE Area51 proposal, I think it's fine to suggest and support changes to the scope here. It may be especially worthwhile to do so if SyntheticBiology.SE is not able to attract sufficient support. Certainly we can reconsider scope in the future if that site does launch, and direct some categories of questions to find more focus there.
However, my advice would be to start in steps rather than chunks. Rather than "interdisciplinary questions" or "biological engineering questions", I'd recommend starting with a close cluster of similar questions that you think are a good fit for the SE format and a good fit for Biology.SE. The big categories are too big: there's too much room for disagreement and too many questions under that bubble that won't fit well. With a more specific focus I think you'll have more luck.
So far, you've linked to two questions that, although they've attracted close-votes and down-votes, have remained open so far and have also received positive votes. It's not clear to me that the community has in fact declared these unacceptable here.
Lastly,
Why would anyone contribute bioengineering content when they get yelled at for doing so?
If someone is yelling, please flag for moderator attention. Including if it's a moderator doing it, and especially if it's me - the other mods will review it.
