Re: everything you know is wrong--again

From: Robert J. Bradbury (
Date: Sun Feb 03 2002 - 16:24:58 MST

On Sun, 3 Feb 2002 wrote:

> Let's consider ourselves a little transcriptor machine, looking to read
> some DNA and make RNA from it. Here's some. Now, which strand is which?
> And which way is "forward"?

To make it even harder -- answer the question -- When you make
an error copying DNA, such that you have base mispairings, how
does the repair machinery know *which* strand is wrong?


> The real mystery to me is why efficiency is seemingly not a factor
> and why junk DNA is allowed to proliferate.

Copying it is relatively cheap compared to the cost of deleting
it and getting it wrong. Since transposons allow easy duplication
of DNA that can subsequently evolved for extended uses retaining
them in the genome allows faster evolution and probably selects
for their retention.

Better questions are whether transposon activation is keyed to
stress as the SOS response is in bacteria and how pufferfish (Fugu)
have managed to keep the junk DNA so low (they only have a 400 MBP
genome which is very small for a vertebrate)?

> But given that efficiency is not an issue, then in hindsight it is
> predictable that both directions and strands could be used.

Yes, but only in viruses and to a lesser extent bacteria do
you see examples of selective pressure to do *really* clever
things like overlapping genes. Getting a piece of DNA
that does one useful thing when read one way and another
useful thing when read another way -- now *thats* real magic!


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