>> I think we need to distinguish between DNA that isn't used for anything,
>> and DNA which actually produces proteins, but they don't do anything
>> really useful.
>>
>> Just having a sequence in your genome doesn't really cost that much.
>> Synthesizing it into a protein is much more expensive.
>>
>> It wouldn't surprise me if non-eukaryotes have fewer genes turned on,
>> and possibly smaller genomes, but I doubt that they have radically
>> "cleaner" genomes.

> You are forgetting that you *still* have to copy all that extra stuff,
> when ever you divide the cell, so there is still a cost to synthesize
> all the copies, before the cell splits to form new cells.

Yes, there is a cost. What I'm saying is that it's a very small cost.

> Also, its not
> a simple case of, "just ignore the stuff I don't use", something has to
> run through the pattern, decide what needs to be unfolded, or folded,
> jump past any stuff that is folded into an unusable state, etc.

It's not like a computer, doing a linear scan of the entire genome 
looking for active genes. It doesn't work like that.

As far as I know (and I'm not an expert on the subject), having extra 
inactive genes imposes very little penalty for transcription.

> And, most of the code, unlike in multi-celled organisms, is going to be
> "on". There is no reason to turn parts off, except for mitosis, and the
> like, if you are not differentiating the cells

False.

Unicellular organisms might not build colonies of differentiated cells, 
but that does *not* mean that all genes are switched on, all the time.

There are organisms that can metabolise both aerobically and 
anaerobically. That's two different metabolic pathways, involving 
different sets of proteins. Many if not most organisms can utilise more 
then one food source. That's different sets of proteins. Many organisms 
have a life-cycle more complex them just "grow, divide, grow, divide". 
That requires different sets of proteins. Some cells even signal each 
other, and undergo limited differentiation under certain conditions. 
More sets of genes. Then there are genes only used in response to attack 
or damage. And so forth.

Seriously. Few if any organisms go around with *all* their genes 
switched on all the time.

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