“However” is perfectly acceptable in scientific writing. It can be used in one of two ways.
1. A quick aside
We found, however, that water is wet.
In this usage, “however” is a way to break up what could be a long technical sentence. As it is a quick aside, two commas are needed on either side of it. This use of “however” is not unlike a verbal tic. Including it is a matter of style. The sentence still makes sense without it, but it does give the sentence a bit of shape, and a comely pause. (Please don’t ask me why pauses are comely. I’m only halfway through my damn coffee.)
2. A U turn
Our hypothesis states that all dogs like steak; however, the sample (n = 44) revealed that only corgi–Doberman mixes ate the steak, while chihuahuas and poodles (n = 20 and 10, respectively) stuck with Kibble and Bits.
Here, the word “however” signals that the sentence is about to go in a whole new direction. As such, it requires both a semi colon and a comma. Each half of the sentence could be its own sentence, but the “however” combines them because it makes sense to do so. The writer is highlighting the fact that her hypothesis said one thing but the evidence revealed something else entirely.
What are your questions?