In science proofs, you can never prove anything, you can only demonstrate that your model describes the data better than another model. You want your alternate hypothesis to come from the new model under test, and the null hypothesis to be from a different model.
The null hypothesis should come from a model which others would choose to use when challenging your scientific claims! The most common pattern for a scientific claim is "I think that X is a factor in process Y. If everyone already believes X is a factor in the process, then there is nothing to prove, and everyone can just go out and talk about it over drinks. Scientific arguments with null hypothesis are interesting because, if someone takes the opposing view, "X is not a factor in process Y, then there is a disagreement. This is where science does its thing.
If you believe "X is a factor in process Y" enough to run an experiment, you should generally know what you're looking to see in the results. So now your phrase becomes "X is a factor in process Y, producing visible outcome Z."
This is where you pick your null hypothesis. If someone believes X is not a factor, and your experiment does indeed show Z, then they need an explanation for Z. With your choice of null hypothesis, you are effectively challenging their explanation. The dead simplest explanation is always "Z was caused by random chance because science is based on statistics." Accordingly, most null hypothesis are in the form of "The outcome should be predicted using the previously accepted model plus some random chance to account for statistics.
Both hypothesis should be phrased in terms of the visible outcome, NOT the model you intend to prove.[note] You never start with an alternate hypothesis of "I believe X is a factor." You phrase it "I expect to see this result when I observe Z." The null hypothesis will be phrased similarly, "The status quo predicts that we will see this different result when I observe Z." There is always a statistical phrasing in there such as "I expect to observe a normal distribution on Z when I do this experiment over and over." Once you observe results that defend your alternate hypothesis and reject the null hypothsis, you are THEN in a position to make claims about the validity of your model.
[note] This bolded statement is my opinion, but I feel confident enough in its wording choice to post it. The hypotheses draw a strong line between the intuitive portion of the science, and the data and analysis of the science. If your phrasing is too close to the model, it becomes hard to separate the model from the data, and makes it harder for the next scientist to use your data
In the case of our simple model with process Y and visible outcome Z, the existing belief is that Z will fit a distribution that everyone is already comfortable with, such as "the randomness expected by your particular laboratory equipment setup" or "the purity of the reagents used in the experiment." When you "reject the null hypothesis" what you are saying is most literally, "I have run this experiment, and it is so tremendously unlikely that random chance generated the observed behavior, that everybody should start considering that maybe there's more to this than meets the eye."
The alternative hypothesis is what you offer to the world to replace the null hypothesis. It is one thing to go do experiments to poke at holes in other's models, but that doesn't promote science nearly as well as poking holes in other's models and then replacing them with new models that do a better job.
With the null and alternate hypothesis, you are trying to challenge the current conventional thinking of the day. Choose the hypotheses so that they effectively declare "Here is a result everybody would expect (null hypothesis). However, I actually went out and did the experiment and gathered data, and it is VERY unlikely that the null hypothesis is true. Here is the result I expected (the alternate hypothesis). Nobody expected this hypothesis to be true but me, but when I gathered the data and did the statistics, it is very likely that my model does a better job of describing reality than the existing model. Accordingly, I reject the null hypothesis, accept my hypothesis, and challenge my fellow scientists to work from this new data."
And the fellow scientists are free to:
- Rejoice and accept your data and model with open arms.
- Ignore your data or model (sorry, it happens... welcome to real life)
- Reject your data, and spend their effort running experiments to show different data (It is very common for the science community to say "We do not trust your sample size of 10. We are going to redo your experiment with a sample size of 1000.)
- Accept your data, but not your model. They then must spend their effort generating a new model which explains the data in a different manner.
The last outcome causes strife and bickering, but is ABSOLUTELY part of the scientific process. By using the scientific method to publish your results, you accept that others are free to use the scientific method to contradict your results. They will do so, and publish their results.
At this point, the scientific community will make a political decision: who has to go out and spend the money to test their model, and whose model do we accept. TYPICALLY, because you published the model and the data first, and they are refuting your data, the onus is on them to run the experiments which proves why their model is better than yours. But this is now WELL beyond the hypothesis that caused the strife in the first place, so I leave you to experience them in your lifetime!