Space can be somewhat inferred by cells through hormone and signaling molecule gradients. So if a central group of cells can start releasing some sort of signaling molecule, and as cells get more distant from that central packet of cells they get less of that molecule, changing their behavior (ie gene expression).

Cells can also divide non-symmetrically, where one cell stays as one type and the other differentiates into a new cell type, creating shape. Cells can pass on information on what genes to express through chemical marks left on the DNA (and the proteins bound to the DNA) telling the new cell what genes to express and what genes to repress.

In the end, though everything does come back to gene expression, which is regulated by a complex network of gene expression networks generated by where the cell originated and what signals it is getting from where it is in the organism.

Interesting the actual genome in the nucleus does have a conserved 3D shape, which has a big impact on how it regulates its genome.

Yes, they can form abiotically and spontaneously, it just requires energy input from the environment (ie heat) at some stage. Also, keep in mind that diphosphates also have energetically favorable dephosphorylation reactions, they just do not work for the biotic enzyme for DNA synthesis.

If you get too deep down this rabbit hole you are going to need a chemist to answer your questions, but here is a review of how the field currently thinks it may have happened.

Yes, as a general rule if it can happen with an enzyme it can happen without an enzyme, enzymes just help things along.

The actual formation of nucleotides is a little more tricky, as that requires energy from the environment. Then you start to delve into deviations from the Miller-Urey experiment and arguments on what is more likely to have happened.

For RNA world to be true, you need to get catalytic activity from a simple repeating molecule, and if that molecule can actually form spontaneously is much more of a question of chance then actual chemical limitations.

Yes, we polymerize nucleotides abiotically all the time wiki. Remember that it is energetically favorable, the enzyme is just positioning things in the right general location.

When things start to get to a certain length we start stitching things together, but that is more of a practical solution than any sort of biochemical limit.

The RNA world hypothesis accounts for this, you are really just researching if you think that it is likely to have happened that way at this point.

I am unaware of any adaptive immune responses in plants (ie what a vaccine would work on). There are some attempts to prime the innate immune responses in order to illicit a stronger response, but that is not a vaccine.

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It is also worth pointing out that we do this on purpose and can modify the proteins we insert into genomes to contain an NLS (Nuclear Localization Sequence).

The last I heard (source) the current thinking was that simple repeat expansion was the source of most de novo mutations, leading to phenotypic changes and symptom severity. This isn't really my field so there might have been a more recent update, but I spend enough time dealing with structural changes to the genome that I read this one when it came out.

Repeat expansion doesn't really behave like a classical mutation, and is more a product of an increased likelihood of specific types of error in DNA replication and repair.

>Is it just the difference in daylight?

Yup, many plants have competing chemical processes triggered by light, darkness, and the wavelengths of light you tend to get in the morning/evening. As the days get shorter this balance shifts and trees leaves start to change color.

>If so how does the tree grow in the spring with similar day lengths?

Plants have a few different strategies here. Some plants do need cold here, as the cold will open access to a gene that was closed off during the fall, allowing them to flower when they days get longer again through a process called vernalization. It is pretty well studied because it occurs in the plant model organism (thale cress).

I am not much of a horticulturist, so I am sure that someone can probably give a much better overview of the different strategies.