When a patent or patent application is published, all the applications it claims priority to (e.g., provisional applications) become open for public inspection.
However, patent applications can act as prior art as of the day they are filed, which is often well before they are published. The justification for this is that, even though the information is not yet public, the applicant has established that they know that information and that it will be disclosed to the public when the patent publishes.
The question in Ariosa Diagnostics v. Illumina is whether the provisional application can also act as prior art as of its filing date. The court's decision was that only the material from the provisional application that was later claimed in the published patent counts as prior art as of the filing date. Everything else in the provisional application only counts as of the publication date.
Patents have two main sections that are very different from each other:
1. The claims set out exactly what inventions the patent protects. They are the part that must be novel and non-obvious. When writing a patent, you want your claims to be as broad as possible (while still satisfying the novelty and non-obviousness requirements) to maximize the protection that the patent offers.
2. The specification teaches a person skilled in the relevant art how to make/use the claimed inventions. This section includes specific details about possible implementations of the inventions. This section can discuss many different variations, and should make it clear that these are only some of the possible variations, not an exhaustive list.
Using a simplistic example based on your child comment, a sentence in the specification might state "The phone may be black, or gold, or any other suitable color." (In reality, the specific color is not likely to be addressed at all unless it plays a role in the claimed invention.)
However, patent applications can act as prior art as of the day they are filed, which is often well before they are published. The justification for this is that, even though the information is not yet public, the applicant has established that they know that information and that it will be disclosed to the public when the patent publishes.
The question in Ariosa Diagnostics v. Illumina is whether the provisional application can also act as prior art as of its filing date. The court's decision was that only the material from the provisional application that was later claimed in the published patent counts as prior art as of the filing date. Everything else in the provisional application only counts as of the publication date.